data_4DK9 # _entry.id 4DK9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4DK9 pdb_00004dk9 10.2210/pdb4dk9/pdb NDB NA1587 ? ? RCSB RCSB070434 ? ? WWPDB D_1000070434 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2012-04-25 2 'Structure model' 1 1 2012-05-16 3 'Structure model' 1 2 2012-07-25 4 'Structure model' 1 3 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_ref_seq_dif 7 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 20 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 21 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 22 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 26 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 27 4 'Structure model' '_struct_ref_seq_dif.details' 28 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 29 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 30 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 4DK9 _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-02-03 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Manvilla, B.A.' 1 'Toth, E.A.' 2 'Drohat, A.C.' 3 # _citation.id primary _citation.title 'Crystal Structure of Human Methyl-Binding Domain IV Glycosylase Bound to Abasic DNA.' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 420 _citation.page_first 164 _citation.page_last 175 _citation.year 2012 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22560993 _citation.pdbx_database_id_DOI 10.1016/j.jmb.2012.04.028 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Manvilla, B.A.' 1 ? primary 'Maiti, A.' 2 ? primary 'Begley, M.C.' 3 ? primary 'Toth, E.A.' 4 ? primary 'Drohat, A.C.' 5 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'" 3407.249 1 ? ? ? 'Complementary DNA strand' 2 polymer syn "5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3'" 3191.073 1 ? ? ? 'Abasic DNA strand' 3 polymer man 'Methyl-CpG-binding domain protein 4' 18671.521 1 3.2.2.- ? 'Catalytic Domain (UNP residues 426-580)' ? 4 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 5 water nat water 18.015 1 ? ? ? ? # _entity_name_com.entity_id 3 _entity_name_com.name 'Methyl-CpG-binding endonuclease 1, Methyl-CpG-binding protein MBD4, Mismatch-specific DNA N-glycosylase' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DA)(DA)(DG)(DA)(DC)(DG)(DT)(DG)(DG)(DA)(DC)' AAGACGTGGAC B ? 2 polydeoxyribonucleotide no yes '(DT)(DG)(DT)(DC)(DC)(DA)(3DR)(DG)(DT)(DC)(DT)' TGTCCANGTCT C ? 3 'polypeptide(L)' no no ;GSALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELL KPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLS ; ;GSALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELL KPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLS ; A ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'POTASSIUM ION' K 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DA n 1 3 DG n 1 4 DA n 1 5 DC n 1 6 DG n 1 7 DT n 1 8 DG n 1 9 DG n 1 10 DA n 1 11 DC n 2 1 DT n 2 2 DG n 2 3 DT n 2 4 DC n 2 5 DC n 2 6 DA n 2 7 3DR n 2 8 DG n 2 9 DT n 2 10 DC n 2 11 DT n 3 1 GLY n 3 2 SER n 3 3 ALA n 3 4 LEU n 3 5 SER n 3 6 PRO n 3 7 PRO n 3 8 ARG n 3 9 ARG n 3 10 LYS n 3 11 ALA n 3 12 PHE n 3 13 LYS n 3 14 LYS n 3 15 TRP n 3 16 THR n 3 17 PRO n 3 18 PRO n 3 19 ARG n 3 20 SER n 3 21 PRO n 3 22 PHE n 3 23 ASN n 3 24 LEU n 3 25 VAL n 3 26 GLN n 3 27 GLU n 3 28 THR n 3 29 LEU n 3 30 PHE n 3 31 HIS n 3 32 ASP n 3 33 PRO n 3 34 TRP n 3 35 LYS n 3 36 LEU n 3 37 LEU n 3 38 ILE n 3 39 ALA n 3 40 THR n 3 41 ILE n 3 42 PHE n 3 43 LEU n 3 44 ASN n 3 45 ARG n 3 46 THR n 3 47 SER n 3 48 GLY n 3 49 LYS n 3 50 MET n 3 51 ALA n 3 52 ILE n 3 53 PRO n 3 54 VAL n 3 55 LEU n 3 56 TRP n 3 57 LYS n 3 58 PHE n 3 59 LEU n 3 60 GLU n 3 61 LYS n 3 62 TYR n 3 63 PRO n 3 64 SER n 3 65 ALA n 3 66 GLU n 3 67 VAL n 3 68 ALA n 3 69 ARG n 3 70 THR n 3 71 ALA n 3 72 ASP n 3 73 TRP n 3 74 ARG n 3 75 ASP n 3 76 VAL n 3 77 SER n 3 78 GLU n 3 79 LEU n 3 80 LEU n 3 81 LYS n 3 82 PRO n 3 83 LEU n 3 84 GLY n 3 85 LEU n 3 86 TYR n 3 87 ASP n 3 88 LEU n 3 89 ARG n 3 90 ALA n 3 91 LYS n 3 92 THR n 3 93 ILE n 3 94 VAL n 3 95 LYS n 3 96 PHE n 3 97 SER n 3 98 ASP n 3 99 GLU n 3 100 TYR n 3 101 LEU n 3 102 THR n 3 103 LYS n 3 104 GLN n 3 105 TRP n 3 106 LYS n 3 107 TYR n 3 108 PRO n 3 109 ILE n 3 110 GLU n 3 111 LEU n 3 112 HIS n 3 113 GLY n 3 114 ILE n 3 115 GLY n 3 116 LYS n 3 117 TYR n 3 118 GLY n 3 119 ASN n 3 120 ASP n 3 121 SER n 3 122 TYR n 3 123 ARG n 3 124 ILE n 3 125 PHE n 3 126 CYS n 3 127 VAL n 3 128 ASN n 3 129 GLU n 3 130 TRP n 3 131 LYS n 3 132 GLN n 3 133 VAL n 3 134 HIS n 3 135 PRO n 3 136 GLU n 3 137 ASP n 3 138 HIS n 3 139 LYS n 3 140 LEU n 3 141 ASN n 3 142 LYS n 3 143 TYR n 3 144 HIS n 3 145 ASP n 3 146 TRP n 3 147 LEU n 3 148 TRP n 3 149 GLU n 3 150 ASN n 3 151 HIS n 3 152 GLU n 3 153 LYS n 3 154 LEU n 3 155 SER n 3 156 LEU n 3 157 SER n # _entity_src_gen.entity_id 3 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'MBD4, MED1' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3) Gold' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 3DR 'DNA linking' . "1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE" 'ABASIC DIDEOXYRIBOSE' 'C5 H11 O6 P' 198.111 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DA 1 1 1 DA DA B . n A 1 2 DA 2 2 2 DA DA B . n A 1 3 DG 3 3 3 DG DG B . n A 1 4 DA 4 4 4 DA DA B . n A 1 5 DC 5 5 5 DC DC B . n A 1 6 DG 6 6 6 DG DG B . n A 1 7 DT 7 7 7 DT DT B . n A 1 8 DG 8 8 8 DG DG B . n A 1 9 DG 9 9 9 DG DG B . n A 1 10 DA 10 10 10 DA DA B . n A 1 11 DC 11 11 11 DC DC B . n B 2 1 DT 1 12 12 DT DT C . n B 2 2 DG 2 13 13 DG DG C . n B 2 3 DT 3 14 14 DT DT C . n B 2 4 DC 4 15 15 DC DC C . n B 2 5 DC 5 16 16 DC DC C . n B 2 6 DA 6 17 17 DA DA C . n B 2 7 3DR 7 18 18 3DR 3DR C . n B 2 8 DG 8 19 19 DG DG C . n B 2 9 DT 9 20 20 DT DT C . n B 2 10 DC 10 21 21 DC DC C . n B 2 11 DT 11 22 22 DT DT C . n C 3 1 GLY 1 424 ? ? ? A . n C 3 2 SER 2 425 ? ? ? A . n C 3 3 ALA 3 426 ? ? ? A . n C 3 4 LEU 4 427 ? ? ? A . n C 3 5 SER 5 428 ? ? ? A . n C 3 6 PRO 6 429 ? ? ? A . n C 3 7 PRO 7 430 ? ? ? A . n C 3 8 ARG 8 431 ? ? ? A . n C 3 9 ARG 9 432 ? ? ? A . n C 3 10 LYS 10 433 ? ? ? A . n C 3 11 ALA 11 434 ? ? ? A . n C 3 12 PHE 12 435 ? ? ? A . n C 3 13 LYS 13 436 ? ? ? A . n C 3 14 LYS 14 437 ? ? ? A . n C 3 15 TRP 15 438 438 TRP TRP A . n C 3 16 THR 16 439 439 THR THR A . n C 3 17 PRO 17 440 440 PRO PRO A . n C 3 18 PRO 18 441 441 PRO PRO A . n C 3 19 ARG 19 442 442 ARG ARG A . n C 3 20 SER 20 443 443 SER SER A . n C 3 21 PRO 21 444 444 PRO PRO A . n C 3 22 PHE 22 445 445 PHE PHE A . n C 3 23 ASN 23 446 446 ASN ASN A . n C 3 24 LEU 24 447 447 LEU LEU A . n C 3 25 VAL 25 448 448 VAL VAL A . n C 3 26 GLN 26 449 449 GLN GLN A . n C 3 27 GLU 27 450 450 GLU GLU A . n C 3 28 THR 28 451 451 THR THR A . n C 3 29 LEU 29 452 452 LEU LEU A . n C 3 30 PHE 30 453 453 PHE PHE A . n C 3 31 HIS 31 454 454 HIS HIS A . n C 3 32 ASP 32 455 455 ASP ASP A . n C 3 33 PRO 33 456 456 PRO PRO A . n C 3 34 TRP 34 457 457 TRP TRP A . n C 3 35 LYS 35 458 458 LYS LYS A . n C 3 36 LEU 36 459 459 LEU LEU A . n C 3 37 LEU 37 460 460 LEU LEU A . n C 3 38 ILE 38 461 461 ILE ILE A . n C 3 39 ALA 39 462 462 ALA ALA A . n C 3 40 THR 40 463 463 THR THR A . n C 3 41 ILE 41 464 464 ILE ILE A . n C 3 42 PHE 42 465 465 PHE PHE A . n C 3 43 LEU 43 466 466 LEU LEU A . n C 3 44 ASN 44 467 467 ASN ASN A . n C 3 45 ARG 45 468 468 ARG ARG A . n C 3 46 THR 46 469 469 THR THR A . n C 3 47 SER 47 470 470 SER SER A . n C 3 48 GLY 48 471 471 GLY GLY A . n C 3 49 LYS 49 472 472 LYS LYS A . n C 3 50 MET 50 473 473 MET MET A . n C 3 51 ALA 51 474 474 ALA ALA A . n C 3 52 ILE 52 475 475 ILE ILE A . n C 3 53 PRO 53 476 476 PRO PRO A . n C 3 54 VAL 54 477 477 VAL VAL A . n C 3 55 LEU 55 478 478 LEU LEU A . n C 3 56 TRP 56 479 479 TRP TRP A . n C 3 57 LYS 57 480 480 LYS LYS A . n C 3 58 PHE 58 481 481 PHE PHE A . n C 3 59 LEU 59 482 482 LEU LEU A . n C 3 60 GLU 60 483 483 GLU GLU A . n C 3 61 LYS 61 484 484 LYS LYS A . n C 3 62 TYR 62 485 485 TYR TYR A . n C 3 63 PRO 63 486 486 PRO PRO A . n C 3 64 SER 64 487 487 SER SER A . n C 3 65 ALA 65 488 488 ALA ALA A . n C 3 66 GLU 66 489 489 GLU GLU A . n C 3 67 VAL 67 490 490 VAL VAL A . n C 3 68 ALA 68 491 491 ALA ALA A . n C 3 69 ARG 69 492 492 ARG ARG A . n C 3 70 THR 70 493 493 THR THR A . n C 3 71 ALA 71 494 494 ALA ALA A . n C 3 72 ASP 72 495 495 ASP ASP A . n C 3 73 TRP 73 496 496 TRP TRP A . n C 3 74 ARG 74 497 497 ARG ARG A . n C 3 75 ASP 75 498 498 ASP ASP A . n C 3 76 VAL 76 499 499 VAL VAL A . n C 3 77 SER 77 500 500 SER SER A . n C 3 78 GLU 78 501 501 GLU GLU A . n C 3 79 LEU 79 502 502 LEU LEU A . n C 3 80 LEU 80 503 503 LEU LEU A . n C 3 81 LYS 81 504 504 LYS LYS A . n C 3 82 PRO 82 505 505 PRO PRO A . n C 3 83 LEU 83 506 506 LEU LEU A . n C 3 84 GLY 84 507 507 GLY GLY A . n C 3 85 LEU 85 508 508 LEU LEU A . n C 3 86 TYR 86 509 509 TYR TYR A . n C 3 87 ASP 87 510 510 ASP ASP A . n C 3 88 LEU 88 511 511 LEU LEU A . n C 3 89 ARG 89 512 512 ARG ARG A . n C 3 90 ALA 90 513 513 ALA ALA A . n C 3 91 LYS 91 514 514 LYS LYS A . n C 3 92 THR 92 515 515 THR THR A . n C 3 93 ILE 93 516 516 ILE ILE A . n C 3 94 VAL 94 517 517 VAL VAL A . n C 3 95 LYS 95 518 518 LYS LYS A . n C 3 96 PHE 96 519 519 PHE PHE A . n C 3 97 SER 97 520 520 SER SER A . n C 3 98 ASP 98 521 521 ASP ASP A . n C 3 99 GLU 99 522 522 GLU GLU A . n C 3 100 TYR 100 523 523 TYR TYR A . n C 3 101 LEU 101 524 524 LEU LEU A . n C 3 102 THR 102 525 525 THR THR A . n C 3 103 LYS 103 526 526 LYS LYS A . n C 3 104 GLN 104 527 527 GLN GLN A . n C 3 105 TRP 105 528 528 TRP TRP A . n C 3 106 LYS 106 529 529 LYS LYS A . n C 3 107 TYR 107 530 530 TYR TYR A . n C 3 108 PRO 108 531 531 PRO PRO A . n C 3 109 ILE 109 532 532 ILE ILE A . n C 3 110 GLU 110 533 533 GLU GLU A . n C 3 111 LEU 111 534 534 LEU LEU A . n C 3 112 HIS 112 535 535 HIS HIS A . n C 3 113 GLY 113 536 536 GLY GLY A . n C 3 114 ILE 114 537 537 ILE ILE A . n C 3 115 GLY 115 538 538 GLY GLY A . n C 3 116 LYS 116 539 539 LYS LYS A . n C 3 117 TYR 117 540 540 TYR TYR A . n C 3 118 GLY 118 541 541 GLY GLY A . n C 3 119 ASN 119 542 542 ASN ASN A . n C 3 120 ASP 120 543 543 ASP ASP A . n C 3 121 SER 121 544 544 SER SER A . n C 3 122 TYR 122 545 545 TYR TYR A . n C 3 123 ARG 123 546 546 ARG ARG A . n C 3 124 ILE 124 547 547 ILE ILE A . n C 3 125 PHE 125 548 548 PHE PHE A . n C 3 126 CYS 126 549 549 CYS CYS A . n C 3 127 VAL 127 550 550 VAL VAL A . n C 3 128 ASN 128 551 551 ASN ASN A . n C 3 129 GLU 129 552 552 GLU GLU A . n C 3 130 TRP 130 553 553 TRP TRP A . n C 3 131 LYS 131 554 554 LYS LYS A . n C 3 132 GLN 132 555 555 GLN GLN A . n C 3 133 VAL 133 556 556 VAL VAL A . n C 3 134 HIS 134 557 557 HIS HIS A . n C 3 135 PRO 135 558 558 PRO PRO A . n C 3 136 GLU 136 559 559 GLU GLU A . n C 3 137 ASP 137 560 560 ASP ASP A . n C 3 138 HIS 138 561 561 HIS HIS A . n C 3 139 LYS 139 562 562 LYS LYS A . n C 3 140 LEU 140 563 563 LEU LEU A . n C 3 141 ASN 141 564 564 ASN ASN A . n C 3 142 LYS 142 565 565 LYS LYS A . n C 3 143 TYR 143 566 566 TYR TYR A . n C 3 144 HIS 144 567 567 HIS HIS A . n C 3 145 ASP 145 568 568 ASP ASP A . n C 3 146 TRP 146 569 569 TRP TRP A . n C 3 147 LEU 147 570 570 LEU LEU A . n C 3 148 TRP 148 571 571 TRP TRP A . n C 3 149 GLU 149 572 572 GLU GLU A . n C 3 150 ASN 150 573 573 ASN ASN A . n C 3 151 HIS 151 574 574 HIS HIS A . n C 3 152 GLU 152 575 575 GLU GLU A . n C 3 153 LYS 153 576 576 LYS LYS A . n C 3 154 LEU 154 577 577 LEU LEU A . n C 3 155 SER 155 578 ? ? ? A . n C 3 156 LEU 156 579 ? ? ? A . n C 3 157 SER 157 580 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 K 1 601 1 K K A . E 5 HOH 1 101 7 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A ARG 442 ? NH1 ? C ARG 19 NH1 2 1 Y 1 A ARG 442 ? NH2 ? C ARG 19 NH2 3 1 Y 1 A SER 470 ? OG ? C SER 47 OG 4 1 Y 1 A LYS 472 ? CD ? C LYS 49 CD 5 1 Y 1 A LYS 472 ? CE ? C LYS 49 CE 6 1 Y 1 A LYS 472 ? NZ ? C LYS 49 NZ 7 1 Y 1 A ILE 475 ? CD1 ? C ILE 52 CD1 8 1 Y 1 A LYS 480 ? CE ? C LYS 57 CE 9 1 Y 1 A LYS 480 ? NZ ? C LYS 57 NZ 10 1 Y 1 A GLU 483 ? CG ? C GLU 60 CG 11 1 Y 1 A GLU 483 ? CD ? C GLU 60 CD 12 1 Y 1 A GLU 483 ? OE1 ? C GLU 60 OE1 13 1 Y 1 A GLU 483 ? OE2 ? C GLU 60 OE2 14 1 Y 1 A LYS 484 ? CE ? C LYS 61 CE 15 1 Y 1 A LYS 484 ? NZ ? C LYS 61 NZ 16 1 Y 1 A ARG 497 ? CD ? C ARG 74 CD 17 1 Y 1 A ARG 497 ? NE ? C ARG 74 NE 18 1 Y 1 A ARG 497 ? CZ ? C ARG 74 CZ 19 1 Y 1 A ARG 497 ? NH1 ? C ARG 74 NH1 20 1 Y 1 A ARG 497 ? NH2 ? C ARG 74 NH2 21 1 Y 1 A LYS 504 ? CG ? C LYS 81 CG 22 1 Y 1 A LYS 504 ? CD ? C LYS 81 CD 23 1 Y 1 A LYS 504 ? CE ? C LYS 81 CE 24 1 Y 1 A LYS 504 ? NZ ? C LYS 81 NZ 25 1 Y 1 A LEU 506 ? CD2 ? C LEU 83 CD2 26 1 Y 1 A LYS 514 ? CE ? C LYS 91 CE 27 1 Y 1 A LYS 514 ? NZ ? C LYS 91 NZ 28 1 Y 1 A LYS 529 ? CE ? C LYS 106 CE 29 1 Y 1 A LYS 529 ? NZ ? C LYS 106 NZ 30 1 Y 1 A GLU 575 ? OE1 ? C GLU 152 OE1 31 1 Y 1 A GLU 575 ? OE2 ? C GLU 152 OE2 32 1 Y 1 A LYS 576 ? CD ? C LYS 153 CD 33 1 Y 1 A LYS 576 ? CE ? C LYS 153 CE 34 1 Y 1 A LYS 576 ? NZ ? C LYS 153 NZ # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 2 PHASER . ? program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 3 REFMAC 5.5.0109 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 4 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 HKL-2000 . ? ? ? ? 'data collection' ? ? ? 6 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? # _cell.length_a 40.999 _cell.length_b 55.161 _cell.length_c 122.193 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 4DK9 _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.entry_id 4DK9 _symmetry.Int_Tables_number 19 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 4DK9 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.73 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 55.01 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.pH ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details '0.2M potassium acetate, 20% PEG 3350, VAPOR DIFFUSION, temperature 298K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54178 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU MICROMAX-007' _diffrn_source.pdbx_wavelength_list 1.54178 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _reflns.entry_id 4DK9 _reflns.d_resolution_high 2.750 _reflns.d_resolution_low 150.000 _reflns.number_obs 7618 _reflns.pdbx_Rmerge_I_obs 0.156 _reflns.pdbx_netI_over_sigmaI 6.700 _reflns.pdbx_chi_squared 0.985 _reflns.pdbx_redundancy 9.800 _reflns.percent_possible_obs 99.900 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.750 2.850 ? ? ? 0.941 ? ? 0.802 9.700 ? 725 100.000 1 1 2.850 2.960 ? ? ? 0.729 ? ? 0.858 9.800 ? 740 100.000 2 1 2.960 3.100 ? ? ? 0.521 ? ? 0.993 10.000 ? 748 100.000 3 1 3.100 3.260 ? ? ? 0.353 ? ? 1.068 10.000 ? 754 100.000 4 1 3.260 3.460 ? ? ? 0.241 ? ? 1.148 10.000 ? 744 100.000 5 1 3.460 3.730 ? ? ? 0.177 ? ? 0.951 10.000 ? 756 100.000 6 1 3.730 4.110 ? ? ? 0.149 ? ? 0.922 10.000 ? 764 100.000 7 1 4.110 4.700 ? ? ? 0.110 ? ? 1.064 9.900 ? 759 100.000 8 1 4.700 5.920 ? ? ? 0.097 ? ? 1.072 9.800 ? 784 100.000 9 1 5.920 150.000 ? ? ? 0.081 ? ? 0.952 9.000 ? 844 98.700 10 1 # _refine.entry_id 4DK9 _refine.ls_d_res_high 2.7600 _refine.ls_d_res_low 61.1000 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.8300 _refine.ls_number_reflns_obs 7583 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.2338 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2594 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.6000 _refine.ls_number_reflns_R_free 350 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 105.3622 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -2.6400 _refine.aniso_B[2][2] 2.8100 _refine.aniso_B[3][3] -0.1700 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9150 _refine.correlation_coeff_Fo_to_Fc_free 0.8970 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.9480 _refine.pdbx_overall_ESU_R_Free 0.3620 _refine.overall_SU_ML 0.3020 _refine.overall_SU_B 34.0070 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 239.530 _refine.B_iso_min 45.000 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1162 _refine_hist.pdbx_number_atoms_nucleic_acid 437 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 1601 _refine_hist.d_res_high 2.7600 _refine_hist.d_res_low 61.1000 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 1694 0.014 0.021 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 2398 1.824 2.262 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 139 6.469 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 56 31.699 23.750 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 188 21.048 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 5 22.732 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 257 0.114 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 1148 0.008 0.021 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 703 4.238 1.500 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 1141 6.114 2.000 ? ? 'X-RAY DIFFRACTION' r_scbond_it 991 2.683 3.000 ? ? 'X-RAY DIFFRACTION' r_scangle_it 1257 4.456 4.500 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 2.7570 _refine_ls_shell.d_res_low 2.8280 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 98.8500 _refine_ls_shell.number_reflns_R_work 494 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.3620 _refine_ls_shell.R_factor_R_free 0.3140 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 22 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 516 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 4DK9 _struct.title 'Crystal Structure of MBD4 Catalytic Domain Bound to Abasic DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4DK9 _struct_keywords.text 'protein-DNA complex, HYDROLASE-DNA complex' _struct_keywords.pdbx_keywords HYDROLASE/DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP MBD4_HUMAN O95243 3 ;ALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKP LGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLS ; 426 ? 2 PDB 4DK9 4DK9 1 ? ? ? 3 PDB 4DK9 4DK9 2 ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4DK9 A 3 ? 157 ? O95243 426 ? 580 ? 426 580 2 2 4DK9 B 1 ? 11 ? 4DK9 1 ? 11 ? 1 11 3 3 4DK9 C 1 ? 11 ? 4DK9 12 ? 22 ? 12 22 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 4DK9 GLY A 1 ? UNP O95243 ? ? 'expression tag' 424 1 1 4DK9 SER A 2 ? UNP O95243 ? ? 'expression tag' 425 2 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3520 ? 1 MORE -13 ? 1 'SSA (A^2)' 9820 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 VAL C 25 ? PHE C 30 ? VAL A 448 PHE A 453 1 ? 6 HELX_P HELX_P2 2 ASP C 32 ? LEU C 43 ? ASP A 455 LEU A 466 1 ? 12 HELX_P HELX_P3 3 SER C 47 ? TYR C 62 ? SER A 470 TYR A 485 1 ? 16 HELX_P HELX_P4 4 SER C 64 ? ARG C 69 ? SER A 487 ARG A 492 1 ? 6 HELX_P HELX_P5 5 ASP C 72 ? LYS C 81 ? ASP A 495 LYS A 504 1 ? 10 HELX_P HELX_P6 6 LEU C 85 ? LYS C 103 ? LEU A 508 LYS A 526 1 ? 19 HELX_P HELX_P7 7 TYR C 107 ? LEU C 111 ? TYR A 530 LEU A 534 5 ? 5 HELX_P HELX_P8 8 GLY C 115 ? CYS C 126 ? GLY A 538 CYS A 549 1 ? 12 HELX_P HELX_P9 9 GLU C 129 ? VAL C 133 ? GLU A 552 VAL A 556 5 ? 5 HELX_P HELX_P10 10 ASP C 137 ? HIS C 151 ? ASP A 560 HIS A 574 1 ? 15 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? B DA 6 "O3'" ? ? ? 1_555 B 3DR 7 P ? ? C DA 17 C 3DR 18 1_555 ? ? ? ? ? ? ? 1.579 ? ? covale2 covale both ? B 3DR 7 "O3'" ? ? ? 1_555 B DG 8 P ? ? C 3DR 18 C DG 19 1_555 ? ? ? ? ? ? ? 1.597 ? ? metalc1 metalc ? ? B DC 10 OP1 ? ? ? 1_555 D K . K ? ? C DC 21 A K 601 1_555 ? ? ? ? ? ? ? 2.782 ? ? metalc2 metalc ? ? C ILE 109 O ? ? ? 1_555 D K . K ? ? A ILE 532 A K 601 1_555 ? ? ? ? ? ? ? 2.744 ? ? metalc3 metalc ? ? C LEU 111 O ? ? ? 1_555 D K . K ? ? A LEU 534 A K 601 1_555 ? ? ? ? ? ? ? 2.613 ? ? metalc4 metalc ? ? C ILE 114 O ? ? ? 1_555 D K . K ? ? A ILE 537 A K 601 1_555 ? ? ? ? ? ? ? 2.645 ? ? hydrog1 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 11 N3 ? ? B DA 2 C DT 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 11 O4 ? ? B DA 2 C DT 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 10 N3 ? ? B DG 3 C DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 10 O2 ? ? B DG 3 C DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 10 N4 ? ? B DG 3 C DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 9 N3 ? ? B DA 4 C DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 9 O4 ? ? B DA 4 C DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 8 N2 ? ? B DC 5 C DG 19 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog9 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? B DT 7 C DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? B DT 7 C DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 8 N1 ? ? ? 1_555 B DC 5 N3 ? ? B DG 8 C DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 8 N2 ? ? ? 1_555 B DC 5 O2 ? ? B DG 8 C DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 8 O6 ? ? ? 1_555 B DC 5 N4 ? ? B DG 8 C DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 4 N3 ? ? B DG 9 C DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 4 O2 ? ? B DG 9 C DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 4 N4 ? ? B DG 9 C DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 10 N1 ? ? ? 1_555 B DT 3 N3 ? ? B DA 10 C DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 3 O4 ? ? B DA 10 C DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? B DC 11 C DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? B DC 11 C DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? B DC 11 C DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP1 ? B DC 10 ? C DC 21 ? 1_555 K ? D K . ? A K 601 ? 1_555 O ? C ILE 109 ? A ILE 532 ? 1_555 167.0 ? 2 OP1 ? B DC 10 ? C DC 21 ? 1_555 K ? D K . ? A K 601 ? 1_555 O ? C LEU 111 ? A LEU 534 ? 1_555 86.1 ? 3 O ? C ILE 109 ? A ILE 532 ? 1_555 K ? D K . ? A K 601 ? 1_555 O ? C LEU 111 ? A LEU 534 ? 1_555 83.6 ? 4 OP1 ? B DC 10 ? C DC 21 ? 1_555 K ? D K . ? A K 601 ? 1_555 O ? C ILE 114 ? A ILE 537 ? 1_555 91.9 ? 5 O ? C ILE 109 ? A ILE 532 ? 1_555 K ? D K . ? A K 601 ? 1_555 O ? C ILE 114 ? A ILE 537 ? 1_555 80.2 ? 6 O ? C LEU 111 ? A LEU 534 ? 1_555 K ? D K . ? A K 601 ? 1_555 O ? C ILE 114 ? A ILE 537 ? 1_555 90.0 ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id LYS _struct_mon_prot_cis.label_seq_id 81 _struct_mon_prot_cis.label_asym_id C _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id LYS _struct_mon_prot_cis.auth_seq_id 504 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 82 _struct_mon_prot_cis.pdbx_label_asym_id_2 C _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 505 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 8.52 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id K _struct_site.pdbx_auth_seq_id 601 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE K A 601' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 ILE C 109 ? ILE A 532 . ? 1_555 ? 2 AC1 4 LEU C 111 ? LEU A 534 . ? 1_555 ? 3 AC1 4 ILE C 114 ? ILE A 537 . ? 1_555 ? 4 AC1 4 DC B 10 ? DC C 21 . ? 1_555 ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_angle.auth_asym_id_1 C _pdbx_validate_rmsd_angle.auth_comp_id_1 3DR _pdbx_validate_rmsd_angle.auth_seq_id_1 18 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 P _pdbx_validate_rmsd_angle.auth_asym_id_2 C _pdbx_validate_rmsd_angle.auth_comp_id_2 DG _pdbx_validate_rmsd_angle.auth_seq_id_2 19 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 OP2 _pdbx_validate_rmsd_angle.auth_asym_id_3 C _pdbx_validate_rmsd_angle.auth_comp_id_3 DG _pdbx_validate_rmsd_angle.auth_seq_id_3 19 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 118.30 _pdbx_validate_rmsd_angle.angle_target_value 110.50 _pdbx_validate_rmsd_angle.angle_deviation 7.80 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.10 _pdbx_validate_rmsd_angle.linker_flag Y # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined -10.5629 13.1560 -15.8617 0.2498 0.2952 0.2745 0.0240 -0.0098 -0.0126 1.8493 0.3620 1.5430 0.2577 -0.4300 -0.0663 0.1787 -0.1320 -0.0467 0.0760 -0.0779 0.0684 -0.0555 -0.0780 0.1054 'X-RAY DIFFRACTION' 2 ? refined -13.6454 32.0644 -21.9874 0.3964 0.2906 0.0708 -0.0527 -0.1164 0.1109 0.9142 2.5311 1.1892 -1.5238 1.5435 -2.0949 -0.2055 0.2048 0.0008 0.2171 -0.1225 0.1188 0.3369 -0.6066 0.0136 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 438 A 576 ? . . . . ? 'X-RAY DIFFRACTION' 2 2 B 1 B 11 ? . . . . ? 'X-RAY DIFFRACTION' 3 2 C 12 C 22 ? . . . . ? # _phasing.method MR # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 424 ? C GLY 1 2 1 Y 1 A SER 425 ? C SER 2 3 1 Y 1 A ALA 426 ? C ALA 3 4 1 Y 1 A LEU 427 ? C LEU 4 5 1 Y 1 A SER 428 ? C SER 5 6 1 Y 1 A PRO 429 ? C PRO 6 7 1 Y 1 A PRO 430 ? C PRO 7 8 1 Y 1 A ARG 431 ? C ARG 8 9 1 Y 1 A ARG 432 ? C ARG 9 10 1 Y 1 A LYS 433 ? C LYS 10 11 1 Y 1 A ALA 434 ? C ALA 11 12 1 Y 1 A PHE 435 ? C PHE 12 13 1 Y 1 A LYS 436 ? C LYS 13 14 1 Y 1 A LYS 437 ? C LYS 14 15 1 Y 1 A SER 578 ? C SER 155 16 1 Y 1 A LEU 579 ? C LEU 156 17 1 Y 1 A SER 580 ? C SER 157 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 3DR "O5'" O N N 1 3DR P P N N 2 3DR OP1 O N N 3 3DR OP2 O N N 4 3DR OP3 O N N 5 3DR "C2'" C N N 6 3DR "C5'" C N N 7 3DR "C4'" C N R 8 3DR "O4'" O N N 9 3DR "C1'" C N N 10 3DR "C3'" C N S 11 3DR "O3'" O N N 12 3DR HOP2 H N N 13 3DR HOP3 H N N 14 3DR "H2'" H N N 15 3DR "H2''" H N N 16 3DR "H5'" H N N 17 3DR "H5''" H N N 18 3DR "H4'1" H N N 19 3DR "H1'1" H N N 20 3DR "H1'2" H N N 21 3DR "H3'" H N N 22 3DR "HO3'" H N N 23 ALA N N N N 24 ALA CA C N S 25 ALA C C N N 26 ALA O O N N 27 ALA CB C N N 28 ALA OXT O N N 29 ALA H H N N 30 ALA H2 H N N 31 ALA HA H N N 32 ALA HB1 H N N 33 ALA HB2 H N N 34 ALA HB3 H N N 35 ALA HXT H N N 36 ARG N N N N 37 ARG CA C N S 38 ARG C C N N 39 ARG O O N N 40 ARG CB C N N 41 ARG CG C N N 42 ARG CD C N N 43 ARG NE N N N 44 ARG CZ C N N 45 ARG NH1 N N N 46 ARG NH2 N N N 47 ARG OXT O N N 48 ARG H H N N 49 ARG H2 H N N 50 ARG HA H N N 51 ARG HB2 H N N 52 ARG HB3 H N N 53 ARG HG2 H N N 54 ARG HG3 H N N 55 ARG HD2 H N N 56 ARG HD3 H N N 57 ARG HE H N N 58 ARG HH11 H N N 59 ARG HH12 H N N 60 ARG HH21 H N N 61 ARG HH22 H N N 62 ARG HXT H N N 63 ASN N N N N 64 ASN CA C N S 65 ASN C C N N 66 ASN O O N N 67 ASN CB C N N 68 ASN CG C N N 69 ASN OD1 O N N 70 ASN ND2 N N N 71 ASN OXT O N N 72 ASN H H N N 73 ASN H2 H N N 74 ASN HA H N N 75 ASN HB2 H N N 76 ASN HB3 H N N 77 ASN HD21 H N N 78 ASN HD22 H N N 79 ASN HXT H N N 80 ASP N N N N 81 ASP CA C N S 82 ASP C C N N 83 ASP O O N N 84 ASP CB C N N 85 ASP CG C N N 86 ASP OD1 O N N 87 ASP OD2 O N N 88 ASP OXT O N N 89 ASP H H N N 90 ASP H2 H N N 91 ASP HA H N N 92 ASP HB2 H N N 93 ASP HB3 H N N 94 ASP HD2 H N N 95 ASP HXT H N N 96 CYS N N N N 97 CYS CA C N R 98 CYS C C N N 99 CYS O O N N 100 CYS CB C N N 101 CYS SG S N N 102 CYS OXT O N N 103 CYS H H N N 104 CYS H2 H N N 105 CYS HA H N N 106 CYS HB2 H N N 107 CYS HB3 H N N 108 CYS HG H N N 109 CYS HXT H N N 110 DA OP3 O N N 111 DA P P N N 112 DA OP1 O N N 113 DA OP2 O N N 114 DA "O5'" O N N 115 DA "C5'" C N N 116 DA "C4'" C N R 117 DA "O4'" O N N 118 DA "C3'" C N S 119 DA "O3'" O N N 120 DA "C2'" C N N 121 DA "C1'" C N R 122 DA N9 N Y N 123 DA C8 C Y N 124 DA N7 N Y N 125 DA C5 C Y N 126 DA C6 C Y N 127 DA N6 N N N 128 DA N1 N Y N 129 DA C2 C Y N 130 DA N3 N Y N 131 DA C4 C Y N 132 DA HOP3 H N N 133 DA HOP2 H N N 134 DA "H5'" H N N 135 DA "H5''" H N N 136 DA "H4'" H N N 137 DA "H3'" H N N 138 DA "HO3'" H N N 139 DA "H2'" H N N 140 DA "H2''" H N N 141 DA "H1'" H N N 142 DA H8 H N N 143 DA H61 H N N 144 DA H62 H N N 145 DA H2 H N N 146 DC OP3 O N N 147 DC P P N N 148 DC OP1 O N N 149 DC OP2 O N N 150 DC "O5'" O N N 151 DC "C5'" C N N 152 DC "C4'" C N R 153 DC "O4'" O N N 154 DC "C3'" C N S 155 DC "O3'" O N N 156 DC "C2'" C N N 157 DC "C1'" C N R 158 DC N1 N N N 159 DC C2 C N N 160 DC O2 O N N 161 DC N3 N N N 162 DC C4 C N N 163 DC N4 N N N 164 DC C5 C N N 165 DC C6 C N N 166 DC HOP3 H N N 167 DC HOP2 H N N 168 DC "H5'" H N N 169 DC "H5''" H N N 170 DC "H4'" H N N 171 DC "H3'" H N N 172 DC "HO3'" H N N 173 DC "H2'" H N N 174 DC "H2''" H N N 175 DC "H1'" H N N 176 DC H41 H N N 177 DC H42 H N N 178 DC H5 H N N 179 DC H6 H N N 180 DG OP3 O N N 181 DG P P N N 182 DG OP1 O N N 183 DG OP2 O N N 184 DG "O5'" O N N 185 DG "C5'" C N N 186 DG "C4'" C N R 187 DG "O4'" O N N 188 DG "C3'" C N S 189 DG "O3'" O N N 190 DG "C2'" C N N 191 DG "C1'" C N R 192 DG N9 N Y N 193 DG C8 C Y N 194 DG N7 N Y N 195 DG C5 C Y N 196 DG C6 C N N 197 DG O6 O N N 198 DG N1 N N N 199 DG C2 C N N 200 DG N2 N N N 201 DG N3 N N N 202 DG C4 C Y N 203 DG HOP3 H N N 204 DG HOP2 H N N 205 DG "H5'" H N N 206 DG "H5''" H N N 207 DG "H4'" H N N 208 DG "H3'" H N N 209 DG "HO3'" H N N 210 DG "H2'" H N N 211 DG "H2''" H N N 212 DG "H1'" H N N 213 DG H8 H N N 214 DG H1 H N N 215 DG H21 H N N 216 DG H22 H N N 217 DT OP3 O N N 218 DT P P N N 219 DT OP1 O N N 220 DT OP2 O N N 221 DT "O5'" O N N 222 DT "C5'" C N N 223 DT "C4'" C N R 224 DT "O4'" O N N 225 DT "C3'" C N S 226 DT "O3'" O N N 227 DT "C2'" C N N 228 DT "C1'" C N R 229 DT N1 N N N 230 DT C2 C N N 231 DT O2 O N N 232 DT N3 N N N 233 DT C4 C N N 234 DT O4 O N N 235 DT C5 C N N 236 DT C7 C N N 237 DT C6 C N N 238 DT HOP3 H N N 239 DT HOP2 H N N 240 DT "H5'" H N N 241 DT "H5''" H N N 242 DT "H4'" H N N 243 DT "H3'" H N N 244 DT "HO3'" H N N 245 DT "H2'" H N N 246 DT "H2''" H N N 247 DT "H1'" H N N 248 DT H3 H N N 249 DT H71 H N N 250 DT H72 H N N 251 DT H73 H N N 252 DT H6 H N N 253 GLN N N N N 254 GLN CA C N S 255 GLN C C N N 256 GLN O O N N 257 GLN CB C N N 258 GLN CG C N N 259 GLN CD C N N 260 GLN OE1 O N N 261 GLN NE2 N N N 262 GLN OXT O N N 263 GLN H H N N 264 GLN H2 H N N 265 GLN HA H N N 266 GLN HB2 H N N 267 GLN HB3 H N N 268 GLN HG2 H N N 269 GLN HG3 H N N 270 GLN HE21 H N N 271 GLN HE22 H N N 272 GLN HXT H N N 273 GLU N N N N 274 GLU CA C N S 275 GLU C C N N 276 GLU O O N N 277 GLU CB C N N 278 GLU CG C N N 279 GLU CD C N N 280 GLU OE1 O N N 281 GLU OE2 O N N 282 GLU OXT O N N 283 GLU H H N N 284 GLU H2 H N N 285 GLU HA H N N 286 GLU HB2 H N N 287 GLU HB3 H N N 288 GLU HG2 H N N 289 GLU HG3 H N N 290 GLU HE2 H N N 291 GLU HXT H N N 292 GLY N N N N 293 GLY CA C N N 294 GLY C C N N 295 GLY O O N N 296 GLY OXT O N N 297 GLY H H N N 298 GLY H2 H N N 299 GLY HA2 H N N 300 GLY HA3 H N N 301 GLY HXT H N N 302 HIS N N N N 303 HIS CA C N S 304 HIS C C N N 305 HIS O O N N 306 HIS CB C N N 307 HIS CG C Y N 308 HIS ND1 N Y N 309 HIS CD2 C Y N 310 HIS CE1 C Y N 311 HIS NE2 N Y N 312 HIS OXT O N N 313 HIS H H N N 314 HIS H2 H N N 315 HIS HA H N N 316 HIS HB2 H N N 317 HIS HB3 H N N 318 HIS HD1 H N N 319 HIS HD2 H N N 320 HIS HE1 H N N 321 HIS HE2 H N N 322 HIS HXT H N N 323 HOH O O N N 324 HOH H1 H N N 325 HOH H2 H N N 326 ILE N N N N 327 ILE CA C N S 328 ILE C C N N 329 ILE O O N N 330 ILE CB C N S 331 ILE CG1 C N N 332 ILE CG2 C N N 333 ILE CD1 C N N 334 ILE OXT O N N 335 ILE H H N N 336 ILE H2 H N N 337 ILE HA H N N 338 ILE HB H N N 339 ILE HG12 H N N 340 ILE HG13 H N N 341 ILE HG21 H N N 342 ILE HG22 H N N 343 ILE HG23 H N N 344 ILE HD11 H N N 345 ILE HD12 H N N 346 ILE HD13 H N N 347 ILE HXT H N N 348 K K K N N 349 LEU N N N N 350 LEU CA C N S 351 LEU C C N N 352 LEU O O N N 353 LEU CB C N N 354 LEU CG C N N 355 LEU CD1 C N N 356 LEU CD2 C N N 357 LEU OXT O N N 358 LEU H H N N 359 LEU H2 H N N 360 LEU HA H N N 361 LEU HB2 H N N 362 LEU HB3 H N N 363 LEU HG H N N 364 LEU HD11 H N N 365 LEU HD12 H N N 366 LEU HD13 H N N 367 LEU HD21 H N N 368 LEU HD22 H N N 369 LEU HD23 H N N 370 LEU HXT H N N 371 LYS N N N N 372 LYS CA C N S 373 LYS C C N N 374 LYS O O N N 375 LYS CB C N N 376 LYS CG C N N 377 LYS CD C N N 378 LYS CE C N N 379 LYS NZ N N N 380 LYS OXT O N N 381 LYS H H N N 382 LYS H2 H N N 383 LYS HA H N N 384 LYS HB2 H N N 385 LYS HB3 H N N 386 LYS HG2 H N N 387 LYS HG3 H N N 388 LYS HD2 H N N 389 LYS HD3 H N N 390 LYS HE2 H N N 391 LYS HE3 H N N 392 LYS HZ1 H N N 393 LYS HZ2 H N N 394 LYS HZ3 H N N 395 LYS HXT H N N 396 MET N N N N 397 MET CA C N S 398 MET C C N N 399 MET O O N N 400 MET CB C N N 401 MET CG C N N 402 MET SD S N N 403 MET CE C N N 404 MET OXT O N N 405 MET H H N N 406 MET H2 H N N 407 MET HA H N N 408 MET HB2 H N N 409 MET HB3 H N N 410 MET HG2 H N N 411 MET HG3 H N N 412 MET HE1 H N N 413 MET HE2 H N N 414 MET HE3 H N N 415 MET HXT H N N 416 PHE N N N N 417 PHE CA C N S 418 PHE C C N N 419 PHE O O N N 420 PHE CB C N N 421 PHE CG C Y N 422 PHE CD1 C Y N 423 PHE CD2 C Y N 424 PHE CE1 C Y N 425 PHE CE2 C Y N 426 PHE CZ C Y N 427 PHE OXT O N N 428 PHE H H N N 429 PHE H2 H N N 430 PHE HA H N N 431 PHE HB2 H N N 432 PHE HB3 H N N 433 PHE HD1 H N N 434 PHE HD2 H N N 435 PHE HE1 H N N 436 PHE HE2 H N N 437 PHE HZ H N N 438 PHE HXT H N N 439 PRO N N N N 440 PRO CA C N S 441 PRO C C N N 442 PRO O O N N 443 PRO CB C N N 444 PRO CG C N N 445 PRO CD C N N 446 PRO OXT O N N 447 PRO H H N N 448 PRO HA H N N 449 PRO HB2 H N N 450 PRO HB3 H N N 451 PRO HG2 H N N 452 PRO HG3 H N N 453 PRO HD2 H N N 454 PRO HD3 H N N 455 PRO HXT H N N 456 SER N N N N 457 SER CA C N S 458 SER C C N N 459 SER O O N N 460 SER CB C N N 461 SER OG O N N 462 SER OXT O N N 463 SER H H N N 464 SER H2 H N N 465 SER HA H N N 466 SER HB2 H N N 467 SER HB3 H N N 468 SER HG H N N 469 SER HXT H N N 470 THR N N N N 471 THR CA C N S 472 THR C C N N 473 THR O O N N 474 THR CB C N R 475 THR OG1 O N N 476 THR CG2 C N N 477 THR OXT O N N 478 THR H H N N 479 THR H2 H N N 480 THR HA H N N 481 THR HB H N N 482 THR HG1 H N N 483 THR HG21 H N N 484 THR HG22 H N N 485 THR HG23 H N N 486 THR HXT H N N 487 TRP N N N N 488 TRP CA C N S 489 TRP C C N N 490 TRP O O N N 491 TRP CB C N N 492 TRP CG C Y N 493 TRP CD1 C Y N 494 TRP CD2 C Y N 495 TRP NE1 N Y N 496 TRP CE2 C Y N 497 TRP CE3 C Y N 498 TRP CZ2 C Y N 499 TRP CZ3 C Y N 500 TRP CH2 C Y N 501 TRP OXT O N N 502 TRP H H N N 503 TRP H2 H N N 504 TRP HA H N N 505 TRP HB2 H N N 506 TRP HB3 H N N 507 TRP HD1 H N N 508 TRP HE1 H N N 509 TRP HE3 H N N 510 TRP HZ2 H N N 511 TRP HZ3 H N N 512 TRP HH2 H N N 513 TRP HXT H N N 514 TYR N N N N 515 TYR CA C N S 516 TYR C C N N 517 TYR O O N N 518 TYR CB C N N 519 TYR CG C Y N 520 TYR CD1 C Y N 521 TYR CD2 C Y N 522 TYR CE1 C Y N 523 TYR CE2 C Y N 524 TYR CZ C Y N 525 TYR OH O N N 526 TYR OXT O N N 527 TYR H H N N 528 TYR H2 H N N 529 TYR HA H N N 530 TYR HB2 H N N 531 TYR HB3 H N N 532 TYR HD1 H N N 533 TYR HD2 H N N 534 TYR HE1 H N N 535 TYR HE2 H N N 536 TYR HH H N N 537 TYR HXT H N N 538 VAL N N N N 539 VAL CA C N S 540 VAL C C N N 541 VAL O O N N 542 VAL CB C N N 543 VAL CG1 C N N 544 VAL CG2 C N N 545 VAL OXT O N N 546 VAL H H N N 547 VAL H2 H N N 548 VAL HA H N N 549 VAL HB H N N 550 VAL HG11 H N N 551 VAL HG12 H N N 552 VAL HG13 H N N 553 VAL HG21 H N N 554 VAL HG22 H N N 555 VAL HG23 H N N 556 VAL HXT H N N 557 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 3DR "O5'" P sing N N 1 3DR "O5'" "C5'" sing N N 2 3DR P OP1 doub N N 3 3DR P OP2 sing N N 4 3DR P OP3 sing N N 5 3DR OP2 HOP2 sing N N 6 3DR OP3 HOP3 sing N N 7 3DR "C2'" "C1'" sing N N 8 3DR "C2'" "C3'" sing N N 9 3DR "C2'" "H2'" sing N N 10 3DR "C2'" "H2''" sing N N 11 3DR "C5'" "C4'" sing N N 12 3DR "C5'" "H5'" sing N N 13 3DR "C5'" "H5''" sing N N 14 3DR "C4'" "O4'" sing N N 15 3DR "C4'" "C3'" sing N N 16 3DR "C4'" "H4'1" sing N N 17 3DR "O4'" "C1'" sing N N 18 3DR "C1'" "H1'1" sing N N 19 3DR "C1'" "H1'2" sing N N 20 3DR "C3'" "O3'" sing N N 21 3DR "C3'" "H3'" sing N N 22 3DR "O3'" "HO3'" sing N N 23 ALA N CA sing N N 24 ALA N H sing N N 25 ALA N H2 sing N N 26 ALA CA C sing N N 27 ALA CA CB sing N N 28 ALA CA HA sing N N 29 ALA C O doub N N 30 ALA C OXT sing N N 31 ALA CB HB1 sing N N 32 ALA CB HB2 sing N N 33 ALA CB HB3 sing N N 34 ALA OXT HXT sing N N 35 ARG N CA sing N N 36 ARG N H sing N N 37 ARG N H2 sing N N 38 ARG CA C sing N N 39 ARG CA CB sing N N 40 ARG CA HA sing N N 41 ARG C O doub N N 42 ARG C OXT sing N N 43 ARG CB CG sing N N 44 ARG CB HB2 sing N N 45 ARG CB HB3 sing N N 46 ARG CG CD sing N N 47 ARG CG HG2 sing N N 48 ARG CG HG3 sing N N 49 ARG CD NE sing N N 50 ARG CD HD2 sing N N 51 ARG CD HD3 sing N N 52 ARG NE CZ sing N N 53 ARG NE HE sing N N 54 ARG CZ NH1 sing N N 55 ARG CZ NH2 doub N N 56 ARG NH1 HH11 sing N N 57 ARG NH1 HH12 sing N N 58 ARG NH2 HH21 sing N N 59 ARG NH2 HH22 sing N N 60 ARG OXT HXT sing N N 61 ASN N CA sing N N 62 ASN N H sing N N 63 ASN N H2 sing N N 64 ASN CA C sing N N 65 ASN CA CB sing N N 66 ASN CA HA sing N N 67 ASN C O doub N N 68 ASN C OXT sing N N 69 ASN CB CG sing N N 70 ASN CB HB2 sing N N 71 ASN CB HB3 sing N N 72 ASN CG OD1 doub N N 73 ASN CG ND2 sing N N 74 ASN ND2 HD21 sing N N 75 ASN ND2 HD22 sing N N 76 ASN OXT HXT sing N N 77 ASP N CA sing N N 78 ASP N H sing N N 79 ASP N H2 sing N N 80 ASP CA C sing N N 81 ASP CA CB sing N N 82 ASP CA HA sing N N 83 ASP C O doub N N 84 ASP C OXT sing N N 85 ASP CB CG sing N N 86 ASP CB HB2 sing N N 87 ASP CB HB3 sing N N 88 ASP CG OD1 doub N N 89 ASP CG OD2 sing N N 90 ASP OD2 HD2 sing N N 91 ASP OXT HXT sing N N 92 CYS N CA sing N N 93 CYS N H sing N N 94 CYS N H2 sing N N 95 CYS CA C sing N N 96 CYS CA CB sing N N 97 CYS CA HA sing N N 98 CYS C O doub N N 99 CYS C OXT sing N N 100 CYS CB SG sing N N 101 CYS CB HB2 sing N N 102 CYS CB HB3 sing N N 103 CYS SG HG sing N N 104 CYS OXT HXT sing N N 105 DA OP3 P sing N N 106 DA OP3 HOP3 sing N N 107 DA P OP1 doub N N 108 DA P OP2 sing N N 109 DA P "O5'" sing N N 110 DA OP2 HOP2 sing N N 111 DA "O5'" "C5'" sing N N 112 DA "C5'" "C4'" sing N N 113 DA "C5'" "H5'" sing N N 114 DA "C5'" "H5''" sing N N 115 DA "C4'" "O4'" sing N N 116 DA "C4'" "C3'" sing N N 117 DA "C4'" "H4'" sing N N 118 DA "O4'" "C1'" sing N N 119 DA "C3'" "O3'" sing N N 120 DA "C3'" "C2'" sing N N 121 DA "C3'" "H3'" sing N N 122 DA "O3'" "HO3'" sing N N 123 DA "C2'" "C1'" sing N N 124 DA "C2'" "H2'" sing N N 125 DA "C2'" "H2''" sing N N 126 DA "C1'" N9 sing N N 127 DA "C1'" "H1'" sing N N 128 DA N9 C8 sing Y N 129 DA N9 C4 sing Y N 130 DA C8 N7 doub Y N 131 DA C8 H8 sing N N 132 DA N7 C5 sing Y N 133 DA C5 C6 sing Y N 134 DA C5 C4 doub Y N 135 DA C6 N6 sing N N 136 DA C6 N1 doub Y N 137 DA N6 H61 sing N N 138 DA N6 H62 sing N N 139 DA N1 C2 sing Y N 140 DA C2 N3 doub Y N 141 DA C2 H2 sing N N 142 DA N3 C4 sing Y N 143 DC OP3 P sing N N 144 DC OP3 HOP3 sing N N 145 DC P OP1 doub N N 146 DC P OP2 sing N N 147 DC P "O5'" sing N N 148 DC OP2 HOP2 sing N N 149 DC "O5'" "C5'" sing N N 150 DC "C5'" "C4'" sing N N 151 DC "C5'" "H5'" sing N N 152 DC "C5'" "H5''" sing N N 153 DC "C4'" "O4'" sing N N 154 DC "C4'" "C3'" sing N N 155 DC "C4'" "H4'" sing N N 156 DC "O4'" "C1'" sing N N 157 DC "C3'" "O3'" sing N N 158 DC "C3'" "C2'" sing N N 159 DC "C3'" "H3'" sing N N 160 DC "O3'" "HO3'" sing N N 161 DC "C2'" "C1'" sing N N 162 DC "C2'" "H2'" sing N N 163 DC "C2'" "H2''" sing N N 164 DC "C1'" N1 sing N N 165 DC "C1'" "H1'" sing N N 166 DC N1 C2 sing N N 167 DC N1 C6 sing N N 168 DC C2 O2 doub N N 169 DC C2 N3 sing N N 170 DC N3 C4 doub N N 171 DC C4 N4 sing N N 172 DC C4 C5 sing N N 173 DC N4 H41 sing N N 174 DC N4 H42 sing N N 175 DC C5 C6 doub N N 176 DC C5 H5 sing N N 177 DC C6 H6 sing N N 178 DG OP3 P sing N N 179 DG OP3 HOP3 sing N N 180 DG P OP1 doub N N 181 DG P OP2 sing N N 182 DG P "O5'" sing N N 183 DG OP2 HOP2 sing N N 184 DG "O5'" "C5'" sing N N 185 DG "C5'" "C4'" sing N N 186 DG "C5'" "H5'" sing N N 187 DG "C5'" "H5''" sing N N 188 DG "C4'" "O4'" sing N N 189 DG "C4'" "C3'" sing N N 190 DG "C4'" "H4'" sing N N 191 DG "O4'" "C1'" sing N N 192 DG "C3'" "O3'" sing N N 193 DG "C3'" "C2'" sing N N 194 DG "C3'" "H3'" sing N N 195 DG "O3'" "HO3'" sing N N 196 DG "C2'" "C1'" sing N N 197 DG "C2'" "H2'" sing N N 198 DG "C2'" "H2''" sing N N 199 DG "C1'" N9 sing N N 200 DG "C1'" "H1'" sing N N 201 DG N9 C8 sing Y N 202 DG N9 C4 sing Y N 203 DG C8 N7 doub Y N 204 DG C8 H8 sing N N 205 DG N7 C5 sing Y N 206 DG C5 C6 sing N N 207 DG C5 C4 doub Y N 208 DG C6 O6 doub N N 209 DG C6 N1 sing N N 210 DG N1 C2 sing N N 211 DG N1 H1 sing N N 212 DG C2 N2 sing N N 213 DG C2 N3 doub N N 214 DG N2 H21 sing N N 215 DG N2 H22 sing N N 216 DG N3 C4 sing N N 217 DT OP3 P sing N N 218 DT OP3 HOP3 sing N N 219 DT P OP1 doub N N 220 DT P OP2 sing N N 221 DT P "O5'" sing N N 222 DT OP2 HOP2 sing N N 223 DT "O5'" "C5'" sing N N 224 DT "C5'" "C4'" sing N N 225 DT "C5'" "H5'" sing N N 226 DT "C5'" "H5''" sing N N 227 DT "C4'" "O4'" sing N N 228 DT "C4'" "C3'" sing N N 229 DT "C4'" "H4'" sing N N 230 DT "O4'" "C1'" sing N N 231 DT "C3'" "O3'" sing N N 232 DT "C3'" "C2'" sing N N 233 DT "C3'" "H3'" sing N N 234 DT "O3'" "HO3'" sing N N 235 DT "C2'" "C1'" sing N N 236 DT "C2'" "H2'" sing N N 237 DT "C2'" "H2''" sing N N 238 DT "C1'" N1 sing N N 239 DT "C1'" "H1'" sing N N 240 DT N1 C2 sing N N 241 DT N1 C6 sing N N 242 DT C2 O2 doub N N 243 DT C2 N3 sing N N 244 DT N3 C4 sing N N 245 DT N3 H3 sing N N 246 DT C4 O4 doub N N 247 DT C4 C5 sing N N 248 DT C5 C7 sing N N 249 DT C5 C6 doub N N 250 DT C7 H71 sing N N 251 DT C7 H72 sing N N 252 DT C7 H73 sing N N 253 DT C6 H6 sing N N 254 GLN N CA sing N N 255 GLN N H sing N N 256 GLN N H2 sing N N 257 GLN CA C sing N N 258 GLN CA CB sing N N 259 GLN CA HA sing N N 260 GLN C O doub N N 261 GLN C OXT sing N N 262 GLN CB CG sing N N 263 GLN CB HB2 sing N N 264 GLN CB HB3 sing N N 265 GLN CG CD sing N N 266 GLN CG HG2 sing N N 267 GLN CG HG3 sing N N 268 GLN CD OE1 doub N N 269 GLN CD NE2 sing N N 270 GLN NE2 HE21 sing N N 271 GLN NE2 HE22 sing N N 272 GLN OXT HXT sing N N 273 GLU N CA sing N N 274 GLU N H sing N N 275 GLU N H2 sing N N 276 GLU CA C sing N N 277 GLU CA CB sing N N 278 GLU CA HA sing N N 279 GLU C O doub N N 280 GLU C OXT sing N N 281 GLU CB CG sing N N 282 GLU CB HB2 sing N N 283 GLU CB HB3 sing N N 284 GLU CG CD sing N N 285 GLU CG HG2 sing N N 286 GLU CG HG3 sing N N 287 GLU CD OE1 doub N N 288 GLU CD OE2 sing N N 289 GLU OE2 HE2 sing N N 290 GLU OXT HXT sing N N 291 GLY N CA sing N N 292 GLY N H sing N N 293 GLY N H2 sing N N 294 GLY CA C sing N N 295 GLY CA HA2 sing N N 296 GLY CA HA3 sing N N 297 GLY C O doub N N 298 GLY C OXT sing N N 299 GLY OXT HXT sing N N 300 HIS N CA sing N N 301 HIS N H sing N N 302 HIS N H2 sing N N 303 HIS CA C sing N N 304 HIS CA CB sing N N 305 HIS CA HA sing N N 306 HIS C O doub N N 307 HIS C OXT sing N N 308 HIS CB CG sing N N 309 HIS CB HB2 sing N N 310 HIS CB HB3 sing N N 311 HIS CG ND1 sing Y N 312 HIS CG CD2 doub Y N 313 HIS ND1 CE1 doub Y N 314 HIS ND1 HD1 sing N N 315 HIS CD2 NE2 sing Y N 316 HIS CD2 HD2 sing N N 317 HIS CE1 NE2 sing Y N 318 HIS CE1 HE1 sing N N 319 HIS NE2 HE2 sing N N 320 HIS OXT HXT sing N N 321 HOH O H1 sing N N 322 HOH O H2 sing N N 323 ILE N CA sing N N 324 ILE N H sing N N 325 ILE N H2 sing N N 326 ILE CA C sing N N 327 ILE CA CB sing N N 328 ILE CA HA sing N N 329 ILE C O doub N N 330 ILE C OXT sing N N 331 ILE CB CG1 sing N N 332 ILE CB CG2 sing N N 333 ILE CB HB sing N N 334 ILE CG1 CD1 sing N N 335 ILE CG1 HG12 sing N N 336 ILE CG1 HG13 sing N N 337 ILE CG2 HG21 sing N N 338 ILE CG2 HG22 sing N N 339 ILE CG2 HG23 sing N N 340 ILE CD1 HD11 sing N N 341 ILE CD1 HD12 sing N N 342 ILE CD1 HD13 sing N N 343 ILE OXT HXT sing N N 344 LEU N CA sing N N 345 LEU N H sing N N 346 LEU N H2 sing N N 347 LEU CA C sing N N 348 LEU CA CB sing N N 349 LEU CA HA sing N N 350 LEU C O doub N N 351 LEU C OXT sing N N 352 LEU CB CG sing N N 353 LEU CB HB2 sing N N 354 LEU CB HB3 sing N N 355 LEU CG CD1 sing N N 356 LEU CG CD2 sing N N 357 LEU CG HG sing N N 358 LEU CD1 HD11 sing N N 359 LEU CD1 HD12 sing N N 360 LEU CD1 HD13 sing N N 361 LEU CD2 HD21 sing N N 362 LEU CD2 HD22 sing N N 363 LEU CD2 HD23 sing N N 364 LEU OXT HXT sing N N 365 LYS N CA sing N N 366 LYS N H sing N N 367 LYS N H2 sing N N 368 LYS CA C sing N N 369 LYS CA CB sing N N 370 LYS CA HA sing N N 371 LYS C O doub N N 372 LYS C OXT sing N N 373 LYS CB CG sing N N 374 LYS CB HB2 sing N N 375 LYS CB HB3 sing N N 376 LYS CG CD sing N N 377 LYS CG HG2 sing N N 378 LYS CG HG3 sing N N 379 LYS CD CE sing N N 380 LYS CD HD2 sing N N 381 LYS CD HD3 sing N N 382 LYS CE NZ sing N N 383 LYS CE HE2 sing N N 384 LYS CE HE3 sing N N 385 LYS NZ HZ1 sing N N 386 LYS NZ HZ2 sing N N 387 LYS NZ HZ3 sing N N 388 LYS OXT HXT sing N N 389 MET N CA sing N N 390 MET N H sing N N 391 MET N H2 sing N N 392 MET CA C sing N N 393 MET CA CB sing N N 394 MET CA HA sing N N 395 MET C O doub N N 396 MET C OXT sing N N 397 MET CB CG sing N N 398 MET CB HB2 sing N N 399 MET CB HB3 sing N N 400 MET CG SD sing N N 401 MET CG HG2 sing N N 402 MET CG HG3 sing N N 403 MET SD CE sing N N 404 MET CE HE1 sing N N 405 MET CE HE2 sing N N 406 MET CE HE3 sing N N 407 MET OXT HXT sing N N 408 PHE N CA sing N N 409 PHE N H sing N N 410 PHE N H2 sing N N 411 PHE CA C sing N N 412 PHE CA CB sing N N 413 PHE CA HA sing N N 414 PHE C O doub N N 415 PHE C OXT sing N N 416 PHE CB CG sing N N 417 PHE CB HB2 sing N N 418 PHE CB HB3 sing N N 419 PHE CG CD1 doub Y N 420 PHE CG CD2 sing Y N 421 PHE CD1 CE1 sing Y N 422 PHE CD1 HD1 sing N N 423 PHE CD2 CE2 doub Y N 424 PHE CD2 HD2 sing N N 425 PHE CE1 CZ doub Y N 426 PHE CE1 HE1 sing N N 427 PHE CE2 CZ sing Y N 428 PHE CE2 HE2 sing N N 429 PHE CZ HZ sing N N 430 PHE OXT HXT sing N N 431 PRO N CA sing N N 432 PRO N CD sing N N 433 PRO N H sing N N 434 PRO CA C sing N N 435 PRO CA CB sing N N 436 PRO CA HA sing N N 437 PRO C O doub N N 438 PRO C OXT sing N N 439 PRO CB CG sing N N 440 PRO CB HB2 sing N N 441 PRO CB HB3 sing N N 442 PRO CG CD sing N N 443 PRO CG HG2 sing N N 444 PRO CG HG3 sing N N 445 PRO CD HD2 sing N N 446 PRO CD HD3 sing N N 447 PRO OXT HXT sing N N 448 SER N CA sing N N 449 SER N H sing N N 450 SER N H2 sing N N 451 SER CA C sing N N 452 SER CA CB sing N N 453 SER CA HA sing N N 454 SER C O doub N N 455 SER C OXT sing N N 456 SER CB OG sing N N 457 SER CB HB2 sing N N 458 SER CB HB3 sing N N 459 SER OG HG sing N N 460 SER OXT HXT sing N N 461 THR N CA sing N N 462 THR N H sing N N 463 THR N H2 sing N N 464 THR CA C sing N N 465 THR CA CB sing N N 466 THR CA HA sing N N 467 THR C O doub N N 468 THR C OXT sing N N 469 THR CB OG1 sing N N 470 THR CB CG2 sing N N 471 THR CB HB sing N N 472 THR OG1 HG1 sing N N 473 THR CG2 HG21 sing N N 474 THR CG2 HG22 sing N N 475 THR CG2 HG23 sing N N 476 THR OXT HXT sing N N 477 TRP N CA sing N N 478 TRP N H sing N N 479 TRP N H2 sing N N 480 TRP CA C sing N N 481 TRP CA CB sing N N 482 TRP CA HA sing N N 483 TRP C O doub N N 484 TRP C OXT sing N N 485 TRP CB CG sing N N 486 TRP CB HB2 sing N N 487 TRP CB HB3 sing N N 488 TRP CG CD1 doub Y N 489 TRP CG CD2 sing Y N 490 TRP CD1 NE1 sing Y N 491 TRP CD1 HD1 sing N N 492 TRP CD2 CE2 doub Y N 493 TRP CD2 CE3 sing Y N 494 TRP NE1 CE2 sing Y N 495 TRP NE1 HE1 sing N N 496 TRP CE2 CZ2 sing Y N 497 TRP CE3 CZ3 doub Y N 498 TRP CE3 HE3 sing N N 499 TRP CZ2 CH2 doub Y N 500 TRP CZ2 HZ2 sing N N 501 TRP CZ3 CH2 sing Y N 502 TRP CZ3 HZ3 sing N N 503 TRP CH2 HH2 sing N N 504 TRP OXT HXT sing N N 505 TYR N CA sing N N 506 TYR N H sing N N 507 TYR N H2 sing N N 508 TYR CA C sing N N 509 TYR CA CB sing N N 510 TYR CA HA sing N N 511 TYR C O doub N N 512 TYR C OXT sing N N 513 TYR CB CG sing N N 514 TYR CB HB2 sing N N 515 TYR CB HB3 sing N N 516 TYR CG CD1 doub Y N 517 TYR CG CD2 sing Y N 518 TYR CD1 CE1 sing Y N 519 TYR CD1 HD1 sing N N 520 TYR CD2 CE2 doub Y N 521 TYR CD2 HD2 sing N N 522 TYR CE1 CZ doub Y N 523 TYR CE1 HE1 sing N N 524 TYR CE2 CZ sing Y N 525 TYR CE2 HE2 sing N N 526 TYR CZ OH sing N N 527 TYR OH HH sing N N 528 TYR OXT HXT sing N N 529 VAL N CA sing N N 530 VAL N H sing N N 531 VAL N H2 sing N N 532 VAL CA C sing N N 533 VAL CA CB sing N N 534 VAL CA HA sing N N 535 VAL C O doub N N 536 VAL C OXT sing N N 537 VAL CB CG1 sing N N 538 VAL CB CG2 sing N N 539 VAL CB HB sing N N 540 VAL CG1 HG11 sing N N 541 VAL CG1 HG12 sing N N 542 VAL CG1 HG13 sing N N 543 VAL CG2 HG21 sing N N 544 VAL CG2 HG22 sing N N 545 VAL CG2 HG23 sing N N 546 VAL OXT HXT sing N N 547 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4DK9 'b-form double helix' 4DK9 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DA 2 1_555 B DT 11 1_555 0.315 -0.592 -0.545 -8.257 -9.029 3.161 1 B_DA2:DT22_C B 2 ? C 22 ? 20 1 1 A DG 3 1_555 B DC 10 1_555 -0.282 -0.405 -0.029 -0.715 -20.336 0.811 2 B_DG3:DC21_C B 3 ? C 21 ? 19 1 1 A DA 4 1_555 B DT 9 1_555 0.289 -0.198 -0.097 -3.888 -5.988 -1.430 3 B_DA4:DT20_C B 4 ? C 20 ? 20 1 1 A DC 5 1_555 B DG 8 1_555 0.870 0.384 -0.283 13.141 -4.820 13.959 4 B_DC5:DG19_C B 5 ? C 19 ? ? 1 1 A DT 7 1_555 B DA 6 1_555 -0.013 -0.199 0.132 -9.779 -19.928 5.250 5 B_DT7:DA17_C B 7 ? C 17 ? 20 1 1 A DG 8 1_555 B DC 5 1_555 -0.633 -0.015 0.018 5.513 -6.224 2.587 6 B_DG8:DC16_C B 8 ? C 16 ? 19 1 1 A DG 9 1_555 B DC 4 1_555 -0.332 -0.205 -0.288 -5.442 -12.130 0.604 7 B_DG9:DC15_C B 9 ? C 15 ? 19 1 1 A DA 10 1_555 B DT 3 1_555 -0.072 -0.029 0.090 1.755 -11.069 -4.833 8 B_DA10:DT14_C B 10 ? C 14 ? 20 1 1 A DC 11 1_555 B DG 2 1_555 0.363 -0.165 -0.386 9.244 -5.219 1.220 9 B_DC11:DG13_C B 11 ? C 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DA 2 1_555 B DT 11 1_555 A DG 3 1_555 B DC 10 1_555 -0.121 0.389 3.151 -6.982 8.206 31.247 -0.686 -0.953 3.106 14.699 12.505 33.009 1 BB_DA2DG3:DC21DT22_CC B 2 ? C 22 ? B 3 ? C 21 ? 1 A DG 3 1_555 B DC 10 1_555 A DA 4 1_555 B DT 9 1_555 -0.256 -0.161 3.417 -1.249 -2.977 38.127 0.146 0.226 3.425 -4.547 1.907 38.259 2 BB_DG3DA4:DT20DC21_CC B 3 ? C 21 ? B 4 ? C 20 ? 1 A DA 4 1_555 B DT 9 1_555 A DC 5 1_555 B DG 8 1_555 0.182 0.543 2.877 2.571 3.227 32.533 0.469 0.071 2.921 5.731 -4.565 32.786 3 BB_DA4DC5:DG19DT20_CC B 4 ? C 20 ? B 5 ? C 19 ? 1 A DT 7 1_555 B DA 6 1_555 A DG 8 1_555 B DC 5 1_555 0.676 1.611 3.014 2.069 6.024 31.555 1.858 -0.859 3.294 10.938 -3.757 32.176 4 BB_DT7DG8:DC16DA17_CC B 7 ? C 17 ? B 8 ? C 16 ? 1 A DG 8 1_555 B DC 5 1_555 A DG 9 1_555 B DC 4 1_555 -1.176 0.358 3.532 -4.712 11.029 36.309 -1.012 1.131 3.606 17.134 7.320 38.175 5 BB_DG8DG9:DC15DC16_CC B 8 ? C 16 ? B 9 ? C 15 ? 1 A DG 9 1_555 B DC 4 1_555 A DA 10 1_555 B DT 3 1_555 -0.385 -0.007 2.982 -2.532 3.593 35.761 -0.478 0.293 2.986 5.824 4.104 36.022 6 BB_DG9DA10:DT14DC15_CC B 9 ? C 15 ? B 10 ? C 14 ? 1 A DA 10 1_555 B DT 3 1_555 A DC 11 1_555 B DG 2 1_555 0.977 -0.161 3.063 4.651 2.971 30.721 -0.839 -0.972 3.144 5.551 -8.690 31.201 7 BB_DA10DC11:DG13DT14_CC B 10 ? C 14 ? B 11 ? C 13 ? # _atom_sites.entry_id 4DK9 _atom_sites.fract_transf_matrix[1][1] 0.024391 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.018129 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.008184 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C K N O P S # loop_