data_1VCD # _entry.id 1VCD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 1VCD pdb_00001vcd 10.2210/pdb1vcd/pdb RCSB RCSB006457 ? ? WWPDB D_1000006457 ? ? # 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 2005-04-26 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-12-27 # _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' 'Version format compliance' 2 3 'Structure model' 'Source and taxonomy' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 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' 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' '_struct_site.pdbx_auth_asym_id' 4 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1VCD _pdbx_database_status.recvd_initial_deposition_date 2004-03-05 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1VC8 't.thermophilus HB8 Ap6A Hydrolase Ndx1-Ap6A Complex' unspecified PDB 1VC9 't.thermophilus HB8 Ap6A hydrolase Ndx1-Mg2+-ATP complex' unspecified TargetDB ttk003001331.1 . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Iwai, T.' 1 'Nakagawa, N.' 2 'Kuramitsu, S.' 3 'Masui, R.' 4 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 5 # _citation.id primary _citation.title 'Crystal Structure of Nudix Protein Ndx1 from Thermus thermophilus HB8 in binary complex with diadenosine hexaphosphate' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Iwai, T.' 1 ? primary 'Nakagawa, N.' 2 ? primary 'Kuramitsu, S.' 3 ? primary 'Masui, R.' 4 ? # 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 man Ndx1 14186.254 2 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 3 non-polymer syn GLYCEROL 92.094 2 ? ? ? ? 4 water nat water 18.015 183 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'MutT/nudix family protein' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;MELGAGGVVFNAKREVLLLRDRMGFWVFPKGHPEPGESLEEAAVREVWEETGVRAEVLLPLYPTRYVNPKGVEREVHWFL MRGEGAPRLEEGMTGAGWFSPEEARALLAFPEDLGLLEVALERLPL ; _entity_poly.pdbx_seq_one_letter_code_can ;MELGAGGVVFNAKREVLLLRDRMGFWVFPKGHPEPGESLEEAAVREVWEETGVRAEVLLPLYPTRYVNPKGVEREVHWFL MRGEGAPRLEEGMTGAGWFSPEEARALLAFPEDLGLLEVALERLPL ; _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ttk003001331.1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 GLYCEROL GOL 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 GLU n 1 3 LEU n 1 4 GLY n 1 5 ALA n 1 6 GLY n 1 7 GLY n 1 8 VAL n 1 9 VAL n 1 10 PHE n 1 11 ASN n 1 12 ALA n 1 13 LYS n 1 14 ARG n 1 15 GLU n 1 16 VAL n 1 17 LEU n 1 18 LEU n 1 19 LEU n 1 20 ARG n 1 21 ASP n 1 22 ARG n 1 23 MET n 1 24 GLY n 1 25 PHE n 1 26 TRP n 1 27 VAL n 1 28 PHE n 1 29 PRO n 1 30 LYS n 1 31 GLY n 1 32 HIS n 1 33 PRO n 1 34 GLU n 1 35 PRO n 1 36 GLY n 1 37 GLU n 1 38 SER n 1 39 LEU n 1 40 GLU n 1 41 GLU n 1 42 ALA n 1 43 ALA n 1 44 VAL n 1 45 ARG n 1 46 GLU n 1 47 VAL n 1 48 TRP n 1 49 GLU n 1 50 GLU n 1 51 THR n 1 52 GLY n 1 53 VAL n 1 54 ARG n 1 55 ALA n 1 56 GLU n 1 57 VAL n 1 58 LEU n 1 59 LEU n 1 60 PRO n 1 61 LEU n 1 62 TYR n 1 63 PRO n 1 64 THR n 1 65 ARG n 1 66 TYR n 1 67 VAL n 1 68 ASN n 1 69 PRO n 1 70 LYS n 1 71 GLY n 1 72 VAL n 1 73 GLU n 1 74 ARG n 1 75 GLU n 1 76 VAL n 1 77 HIS n 1 78 TRP n 1 79 PHE n 1 80 LEU n 1 81 MET n 1 82 ARG n 1 83 GLY n 1 84 GLU n 1 85 GLY n 1 86 ALA n 1 87 PRO n 1 88 ARG n 1 89 LEU n 1 90 GLU n 1 91 GLU n 1 92 GLY n 1 93 MET n 1 94 THR n 1 95 GLY n 1 96 ALA n 1 97 GLY n 1 98 TRP n 1 99 PHE n 1 100 SER n 1 101 PRO n 1 102 GLU n 1 103 GLU n 1 104 ALA n 1 105 ARG n 1 106 ALA n 1 107 LEU n 1 108 LEU n 1 109 ALA n 1 110 PHE n 1 111 PRO n 1 112 GLU n 1 113 ASP n 1 114 LEU n 1 115 GLY n 1 116 LEU n 1 117 LEU n 1 118 GLU n 1 119 VAL n 1 120 ALA n 1 121 LEU n 1 122 GLU n 1 123 ARG n 1 124 LEU n 1 125 PRO n 1 126 LEU n # _entity_src_gen.entity_id 1 _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 ? _entity_src_gen.gene_src_genus Thermus _entity_src_gen.pdbx_gene_src_gene ndx1 _entity_src_gen.gene_src_species 'Thermus thermophilus' _entity_src_gen.gene_src_strain HB8 _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 'Thermus thermophilus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 300852 _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species 'Escherichia coli' _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _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 PET11B _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 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 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 MET 1 1 1 MET MET A . n A 1 2 GLU 2 2 2 GLU GLU A . n A 1 3 LEU 3 3 3 LEU LEU A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 ALA 5 5 5 ALA ALA A . n A 1 6 GLY 6 6 6 GLY GLY A . n A 1 7 GLY 7 7 7 GLY GLY A . n A 1 8 VAL 8 8 8 VAL VAL A . n A 1 9 VAL 9 9 9 VAL VAL A . n A 1 10 PHE 10 10 10 PHE PHE A . n A 1 11 ASN 11 11 11 ASN ASN A . n A 1 12 ALA 12 12 12 ALA ALA A . n A 1 13 LYS 13 13 13 LYS LYS A . n A 1 14 ARG 14 14 14 ARG ARG A . n A 1 15 GLU 15 15 15 GLU GLU A . n A 1 16 VAL 16 16 16 VAL VAL A . n A 1 17 LEU 17 17 17 LEU LEU A . n A 1 18 LEU 18 18 18 LEU LEU A . n A 1 19 LEU 19 19 19 LEU LEU A . n A 1 20 ARG 20 20 20 ARG ARG A . n A 1 21 ASP 21 21 21 ASP ASP A . n A 1 22 ARG 22 22 22 ARG ARG A . n A 1 23 MET 23 23 23 MET MET A . n A 1 24 GLY 24 24 24 GLY GLY A . n A 1 25 PHE 25 25 25 PHE PHE A . n A 1 26 TRP 26 26 26 TRP TRP A . n A 1 27 VAL 27 27 27 VAL VAL A . n A 1 28 PHE 28 28 28 PHE PHE A . n A 1 29 PRO 29 29 29 PRO PRO A . n A 1 30 LYS 30 30 30 LYS LYS A . n A 1 31 GLY 31 31 31 GLY GLY A . n A 1 32 HIS 32 32 32 HIS HIS A . n A 1 33 PRO 33 33 33 PRO PRO A . n A 1 34 GLU 34 34 34 GLU GLU A . n A 1 35 PRO 35 35 35 PRO PRO A . n A 1 36 GLY 36 36 36 GLY GLY A . n A 1 37 GLU 37 37 37 GLU GLU A . n A 1 38 SER 38 38 38 SER SER A . n A 1 39 LEU 39 39 39 LEU LEU A . n A 1 40 GLU 40 40 40 GLU GLU A . n A 1 41 GLU 41 41 41 GLU GLU A . n A 1 42 ALA 42 42 42 ALA ALA A . n A 1 43 ALA 43 43 43 ALA ALA A . n A 1 44 VAL 44 44 44 VAL VAL A . n A 1 45 ARG 45 45 45 ARG ARG A . n A 1 46 GLU 46 46 46 GLU GLU A . n A 1 47 VAL 47 47 47 VAL VAL A . n A 1 48 TRP 48 48 48 TRP TRP A . n A 1 49 GLU 49 49 49 GLU GLU A . n A 1 50 GLU 50 50 50 GLU GLU A . n A 1 51 THR 51 51 51 THR THR A . n A 1 52 GLY 52 52 52 GLY GLY A . n A 1 53 VAL 53 53 53 VAL VAL A . n A 1 54 ARG 54 54 54 ARG ARG A . n A 1 55 ALA 55 55 55 ALA ALA A . n A 1 56 GLU 56 56 56 GLU GLU A . n A 1 57 VAL 57 57 57 VAL VAL A . n A 1 58 LEU 58 58 58 LEU LEU A . n A 1 59 LEU 59 59 59 LEU LEU A . n A 1 60 PRO 60 60 60 PRO PRO A . n A 1 61 LEU 61 61 61 LEU LEU A . n A 1 62 TYR 62 62 62 TYR TYR A . n A 1 63 PRO 63 63 63 PRO PRO A . n A 1 64 THR 64 64 64 THR THR A . n A 1 65 ARG 65 65 65 ARG ARG A . n A 1 66 TYR 66 66 66 TYR TYR A . n A 1 67 VAL 67 67 67 VAL VAL A . n A 1 68 ASN 68 68 68 ASN ASN A . n A 1 69 PRO 69 69 69 PRO PRO A . n A 1 70 LYS 70 70 70 LYS LYS A . n A 1 71 GLY 71 71 71 GLY GLY A . n A 1 72 VAL 72 72 72 VAL VAL A . n A 1 73 GLU 73 73 73 GLU GLU A . n A 1 74 ARG 74 74 74 ARG ARG A . n A 1 75 GLU 75 75 75 GLU GLU A . n A 1 76 VAL 76 76 76 VAL VAL A . n A 1 77 HIS 77 77 77 HIS HIS A . n A 1 78 TRP 78 78 78 TRP TRP A . n A 1 79 PHE 79 79 79 PHE PHE A . n A 1 80 LEU 80 80 80 LEU LEU A . n A 1 81 MET 81 81 81 MET MET A . n A 1 82 ARG 82 82 82 ARG ARG A . n A 1 83 GLY 83 83 83 GLY GLY A . n A 1 84 GLU 84 84 84 GLU GLU A . n A 1 85 GLY 85 85 85 GLY GLY A . n A 1 86 ALA 86 86 86 ALA ALA A . n A 1 87 PRO 87 87 87 PRO PRO A . n A 1 88 ARG 88 88 88 ARG ARG A . n A 1 89 LEU 89 89 89 LEU LEU A . n A 1 90 GLU 90 90 90 GLU GLU A . n A 1 91 GLU 91 91 91 GLU GLU A . n A 1 92 GLY 92 92 92 GLY GLY A . n A 1 93 MET 93 93 93 MET MET A . n A 1 94 THR 94 94 94 THR THR A . n A 1 95 GLY 95 95 95 GLY GLY A . n A 1 96 ALA 96 96 96 ALA ALA A . n A 1 97 GLY 97 97 97 GLY GLY A . n A 1 98 TRP 98 98 98 TRP TRP A . n A 1 99 PHE 99 99 99 PHE PHE A . n A 1 100 SER 100 100 100 SER SER A . n A 1 101 PRO 101 101 101 PRO PRO A . n A 1 102 GLU 102 102 102 GLU GLU A . n A 1 103 GLU 103 103 103 GLU GLU A . n A 1 104 ALA 104 104 104 ALA ALA A . n A 1 105 ARG 105 105 105 ARG ARG A . n A 1 106 ALA 106 106 106 ALA ALA A . n A 1 107 LEU 107 107 107 LEU LEU A . n A 1 108 LEU 108 108 108 LEU LEU A . n A 1 109 ALA 109 109 109 ALA ALA A . n A 1 110 PHE 110 110 110 PHE PHE A . n A 1 111 PRO 111 111 111 PRO PRO A . n A 1 112 GLU 112 112 112 GLU GLU A . n A 1 113 ASP 113 113 113 ASP ASP A . n A 1 114 LEU 114 114 114 LEU LEU A . n A 1 115 GLY 115 115 115 GLY GLY A . n A 1 116 LEU 116 116 116 LEU LEU A . n A 1 117 LEU 117 117 117 LEU LEU A . n A 1 118 GLU 118 118 118 GLU GLU A . n A 1 119 VAL 119 119 119 VAL VAL A . n A 1 120 ALA 120 120 120 ALA ALA A . n A 1 121 LEU 121 121 121 LEU LEU A . n A 1 122 GLU 122 122 122 GLU GLU A . n A 1 123 ARG 123 123 123 ARG ARG A . n A 1 124 LEU 124 124 124 LEU LEU A . n A 1 125 PRO 125 125 125 PRO PRO A . n A 1 126 LEU 126 126 126 LEU LEU A . n B 1 1 MET 1 1 1 MET MET B . n B 1 2 GLU 2 2 2 GLU GLU B . n B 1 3 LEU 3 3 3 LEU LEU B . n B 1 4 GLY 4 4 4 GLY GLY B . n B 1 5 ALA 5 5 5 ALA ALA B . n B 1 6 GLY 6 6 6 GLY GLY B . n B 1 7 GLY 7 7 7 GLY GLY B . n B 1 8 VAL 8 8 8 VAL VAL B . n B 1 9 VAL 9 9 9 VAL VAL B . n B 1 10 PHE 10 10 10 PHE PHE B . n B 1 11 ASN 11 11 11 ASN ASN B . n B 1 12 ALA 12 12 12 ALA ALA B . n B 1 13 LYS 13 13 13 LYS LYS B . n B 1 14 ARG 14 14 14 ARG ARG B . n B 1 15 GLU 15 15 15 GLU GLU B . n B 1 16 VAL 16 16 16 VAL VAL B . n B 1 17 LEU 17 17 17 LEU LEU B . n B 1 18 LEU 18 18 18 LEU LEU B . n B 1 19 LEU 19 19 19 LEU LEU B . n B 1 20 ARG 20 20 20 ARG ARG B . n B 1 21 ASP 21 21 21 ASP ASP B . n B 1 22 ARG 22 22 22 ARG ARG B . n B 1 23 MET 23 23 23 MET MET B . n B 1 24 GLY 24 24 24 GLY GLY B . n B 1 25 PHE 25 25 25 PHE PHE B . n B 1 26 TRP 26 26 26 TRP TRP B . n B 1 27 VAL 27 27 27 VAL VAL B . n B 1 28 PHE 28 28 28 PHE PHE B . n B 1 29 PRO 29 29 29 PRO PRO B . n B 1 30 LYS 30 30 30 LYS LYS B . n B 1 31 GLY 31 31 31 GLY GLY B . n B 1 32 HIS 32 32 32 HIS HIS B . n B 1 33 PRO 33 33 33 PRO PRO B . n B 1 34 GLU 34 34 34 GLU GLU B . n B 1 35 PRO 35 35 35 PRO PRO B . n B 1 36 GLY 36 36 36 GLY GLY B . n B 1 37 GLU 37 37 37 GLU GLU B . n B 1 38 SER 38 38 38 SER SER B . n B 1 39 LEU 39 39 39 LEU LEU B . n B 1 40 GLU 40 40 40 GLU GLU B . n B 1 41 GLU 41 41 41 GLU GLU B . n B 1 42 ALA 42 42 42 ALA ALA B . n B 1 43 ALA 43 43 43 ALA ALA B . n B 1 44 VAL 44 44 44 VAL VAL B . n B 1 45 ARG 45 45 45 ARG ARG B . n B 1 46 GLU 46 46 46 GLU GLU B . n B 1 47 VAL 47 47 47 VAL VAL B . n B 1 48 TRP 48 48 48 TRP TRP B . n B 1 49 GLU 49 49 49 GLU GLU B . n B 1 50 GLU 50 50 50 GLU GLU B . n B 1 51 THR 51 51 51 THR THR B . n B 1 52 GLY 52 52 52 GLY GLY B . n B 1 53 VAL 53 53 53 VAL VAL B . n B 1 54 ARG 54 54 54 ARG ARG B . n B 1 55 ALA 55 55 55 ALA ALA B . n B 1 56 GLU 56 56 56 GLU GLU B . n B 1 57 VAL 57 57 57 VAL VAL B . n B 1 58 LEU 58 58 58 LEU LEU B . n B 1 59 LEU 59 59 59 LEU LEU B . n B 1 60 PRO 60 60 60 PRO PRO B . n B 1 61 LEU 61 61 61 LEU LEU B . n B 1 62 TYR 62 62 62 TYR TYR B . n B 1 63 PRO 63 63 63 PRO PRO B . n B 1 64 THR 64 64 64 THR THR B . n B 1 65 ARG 65 65 65 ARG ARG B . n B 1 66 TYR 66 66 66 TYR TYR B . n B 1 67 VAL 67 67 67 VAL VAL B . n B 1 68 ASN 68 68 68 ASN ASN B . n B 1 69 PRO 69 69 69 PRO PRO B . n B 1 70 LYS 70 70 70 LYS LYS B . n B 1 71 GLY 71 71 71 GLY GLY B . n B 1 72 VAL 72 72 72 VAL VAL B . n B 1 73 GLU 73 73 73 GLU GLU B . n B 1 74 ARG 74 74 74 ARG ARG B . n B 1 75 GLU 75 75 75 GLU GLU B . n B 1 76 VAL 76 76 76 VAL VAL B . n B 1 77 HIS 77 77 77 HIS HIS B . n B 1 78 TRP 78 78 78 TRP TRP B . n B 1 79 PHE 79 79 79 PHE PHE B . n B 1 80 LEU 80 80 80 LEU LEU B . n B 1 81 MET 81 81 81 MET MET B . n B 1 82 ARG 82 82 82 ARG ARG B . n B 1 83 GLY 83 83 83 GLY GLY B . n B 1 84 GLU 84 84 84 GLU GLU B . n B 1 85 GLY 85 85 85 GLY GLY B . n B 1 86 ALA 86 86 86 ALA ALA B . n B 1 87 PRO 87 87 87 PRO PRO B . n B 1 88 ARG 88 88 88 ARG ARG B . n B 1 89 LEU 89 89 89 LEU LEU B . n B 1 90 GLU 90 90 90 GLU GLU B . n B 1 91 GLU 91 91 91 GLU GLU B . n B 1 92 GLY 92 92 92 GLY GLY B . n B 1 93 MET 93 93 93 MET MET B . n B 1 94 THR 94 94 94 THR THR B . n B 1 95 GLY 95 95 95 GLY GLY B . n B 1 96 ALA 96 96 96 ALA ALA B . n B 1 97 GLY 97 97 97 GLY GLY B . n B 1 98 TRP 98 98 98 TRP TRP B . n B 1 99 PHE 99 99 99 PHE PHE B . n B 1 100 SER 100 100 100 SER SER B . n B 1 101 PRO 101 101 101 PRO PRO B . n B 1 102 GLU 102 102 102 GLU GLU B . n B 1 103 GLU 103 103 103 GLU GLU B . n B 1 104 ALA 104 104 104 ALA ALA B . n B 1 105 ARG 105 105 105 ARG ARG B . n B 1 106 ALA 106 106 106 ALA ALA B . n B 1 107 LEU 107 107 107 LEU LEU B . n B 1 108 LEU 108 108 108 LEU LEU B . n B 1 109 ALA 109 109 109 ALA ALA B . n B 1 110 PHE 110 110 110 PHE PHE B . n B 1 111 PRO 111 111 111 PRO PRO B . n B 1 112 GLU 112 112 112 GLU GLU B . n B 1 113 ASP 113 113 113 ASP ASP B . n B 1 114 LEU 114 114 114 LEU LEU B . n B 1 115 GLY 115 115 115 GLY GLY B . n B 1 116 LEU 116 116 116 LEU LEU B . n B 1 117 LEU 117 117 117 LEU LEU B . n B 1 118 GLU 118 118 118 GLU GLU B . n B 1 119 VAL 119 119 119 VAL VAL B . n B 1 120 ALA 120 120 120 ALA ALA B . n B 1 121 LEU 121 121 121 LEU LEU B . n B 1 122 GLU 122 122 122 GLU GLU B . n B 1 123 ARG 123 123 123 ARG ARG B . n B 1 124 LEU 124 124 124 LEU LEU B . n B 1 125 PRO 125 125 125 PRO PRO B . n B 1 126 LEU 126 126 126 LEU LEU B . 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 C 2 SO4 1 1002 2 SO4 SO4 A . D 3 GOL 1 2001 1 GOL GOL A . E 2 SO4 1 1001 1 SO4 SO4 B . F 3 GOL 1 2002 2 GOL GOL B . G 4 HOH 1 2002 5 HOH TIP A . G 4 HOH 2 2003 6 HOH TIP A . G 4 HOH 3 2004 7 HOH TIP A . G 4 HOH 4 2005 8 HOH TIP A . G 4 HOH 5 2006 9 HOH TIP A . G 4 HOH 6 2007 11 HOH TIP A . G 4 HOH 7 2008 16 HOH TIP A . G 4 HOH 8 2009 19 HOH TIP A . G 4 HOH 9 2010 20 HOH TIP A . G 4 HOH 10 2011 21 HOH TIP A . G 4 HOH 11 2012 25 HOH TIP A . G 4 HOH 12 2013 28 HOH TIP A . G 4 HOH 13 2014 30 HOH TIP A . G 4 HOH 14 2015 35 HOH TIP A . G 4 HOH 15 2016 39 HOH TIP A . G 4 HOH 16 2017 41 HOH TIP A . G 4 HOH 17 2018 43 HOH TIP A . G 4 HOH 18 2019 48 HOH TIP A . G 4 HOH 19 2020 51 HOH TIP A . G 4 HOH 20 2021 52 HOH TIP A . G 4 HOH 21 2022 54 HOH TIP A . G 4 HOH 22 2023 57 HOH TIP A . G 4 HOH 23 2024 61 HOH TIP A . G 4 HOH 24 2025 64 HOH TIP A . G 4 HOH 25 2026 65 HOH TIP A . G 4 HOH 26 2027 66 HOH TIP A . G 4 HOH 27 2028 67 HOH TIP A . G 4 HOH 28 2029 70 HOH TIP A . G 4 HOH 29 2030 72 HOH TIP A . G 4 HOH 30 2031 74 HOH TIP A . G 4 HOH 31 2032 75 HOH TIP A . G 4 HOH 32 2033 77 HOH TIP A . G 4 HOH 33 2034 80 HOH TIP A . G 4 HOH 34 2035 81 HOH TIP A . G 4 HOH 35 2036 82 HOH TIP A . G 4 HOH 36 2037 83 HOH TIP A . G 4 HOH 37 2038 84 HOH TIP A . G 4 HOH 38 2039 87 HOH TIP A . G 4 HOH 39 2040 89 HOH TIP A . G 4 HOH 40 2041 90 HOH TIP A . G 4 HOH 41 2042 92 HOH TIP A . G 4 HOH 42 2043 94 HOH TIP A . G 4 HOH 43 2044 97 HOH TIP A . G 4 HOH 44 2045 101 HOH TIP A . G 4 HOH 45 2046 103 HOH TIP A . G 4 HOH 46 2047 104 HOH TIP A . G 4 HOH 47 2048 107 HOH TIP A . G 4 HOH 48 2049 108 HOH TIP A . G 4 HOH 49 2050 110 HOH TIP A . G 4 HOH 50 2051 114 HOH TIP A . G 4 HOH 51 2052 115 HOH TIP A . G 4 HOH 52 2053 118 HOH TIP A . G 4 HOH 53 2054 120 HOH TIP A . G 4 HOH 54 2055 121 HOH TIP A . G 4 HOH 55 2056 125 HOH TIP A . G 4 HOH 56 2057 127 HOH TIP A . G 4 HOH 57 2058 129 HOH TIP A . G 4 HOH 58 2059 133 HOH TIP A . G 4 HOH 59 2060 136 HOH TIP A . G 4 HOH 60 2061 137 HOH TIP A . G 4 HOH 61 2062 138 HOH TIP A . G 4 HOH 62 2063 140 HOH TIP A . G 4 HOH 63 2064 143 HOH TIP A . G 4 HOH 64 2065 144 HOH TIP A . G 4 HOH 65 2066 147 HOH TIP A . G 4 HOH 66 2067 148 HOH TIP A . G 4 HOH 67 2068 149 HOH TIP A . G 4 HOH 68 2069 150 HOH TIP A . G 4 HOH 69 2070 153 HOH TIP A . G 4 HOH 70 2071 154 HOH TIP A . G 4 HOH 71 2072 157 HOH TIP A . G 4 HOH 72 2073 158 HOH TIP A . G 4 HOH 73 2074 159 HOH TIP A . G 4 HOH 74 2075 164 HOH TIP A . G 4 HOH 75 2076 170 HOH TIP A . G 4 HOH 76 2077 173 HOH TIP A . G 4 HOH 77 2078 175 HOH TIP A . G 4 HOH 78 2079 176 HOH TIP A . G 4 HOH 79 2080 178 HOH TIP A . G 4 HOH 80 2081 182 HOH TIP A . G 4 HOH 81 2082 184 HOH TIP A . H 4 HOH 1 2003 1 HOH TIP B . H 4 HOH 2 2004 2 HOH TIP B . H 4 HOH 3 2005 3 HOH TIP B . H 4 HOH 4 2006 4 HOH TIP B . H 4 HOH 5 2007 10 HOH TIP B . H 4 HOH 6 2008 12 HOH TIP B . H 4 HOH 7 2009 13 HOH TIP B . H 4 HOH 8 2010 15 HOH TIP B . H 4 HOH 9 2011 17 HOH TIP B . H 4 HOH 10 2012 18 HOH TIP B . H 4 HOH 11 2013 22 HOH TIP B . H 4 HOH 12 2014 23 HOH TIP B . H 4 HOH 13 2015 24 HOH TIP B . H 4 HOH 14 2016 26 HOH TIP B . H 4 HOH 15 2017 29 HOH TIP B . H 4 HOH 16 2018 31 HOH TIP B . H 4 HOH 17 2019 32 HOH TIP B . H 4 HOH 18 2020 33 HOH TIP B . H 4 HOH 19 2021 34 HOH TIP B . H 4 HOH 20 2022 36 HOH TIP B . H 4 HOH 21 2023 37 HOH TIP B . H 4 HOH 22 2024 38 HOH TIP B . H 4 HOH 23 2025 40 HOH TIP B . H 4 HOH 24 2026 42 HOH TIP B . H 4 HOH 25 2027 44 HOH TIP B . H 4 HOH 26 2028 45 HOH TIP B . H 4 HOH 27 2029 46 HOH TIP B . H 4 HOH 28 2030 47 HOH TIP B . H 4 HOH 29 2031 49 HOH TIP B . H 4 HOH 30 2032 50 HOH TIP B . H 4 HOH 31 2033 53 HOH TIP B . H 4 HOH 32 2034 55 HOH TIP B . H 4 HOH 33 2035 56 HOH TIP B . H 4 HOH 34 2036 58 HOH TIP B . H 4 HOH 35 2037 59 HOH TIP B . H 4 HOH 36 2038 60 HOH TIP B . H 4 HOH 37 2039 62 HOH TIP B . H 4 HOH 38 2040 68 HOH TIP B . H 4 HOH 39 2041 69 HOH TIP B . H 4 HOH 40 2042 71 HOH TIP B . H 4 HOH 41 2043 73 HOH TIP B . H 4 HOH 42 2044 76 HOH TIP B . H 4 HOH 43 2045 79 HOH TIP B . H 4 HOH 44 2046 85 HOH TIP B . H 4 HOH 45 2047 86 HOH TIP B . H 4 HOH 46 2048 88 HOH TIP B . H 4 HOH 47 2049 91 HOH TIP B . H 4 HOH 48 2050 93 HOH TIP B . H 4 HOH 49 2051 95 HOH TIP B . H 4 HOH 50 2052 96 HOH TIP B . H 4 HOH 51 2053 98 HOH TIP B . H 4 HOH 52 2054 99 HOH TIP B . H 4 HOH 53 2055 100 HOH TIP B . H 4 HOH 54 2056 102 HOH TIP B . H 4 HOH 55 2057 105 HOH TIP B . H 4 HOH 56 2058 106 HOH TIP B . H 4 HOH 57 2059 109 HOH TIP B . H 4 HOH 58 2060 111 HOH TIP B . H 4 HOH 59 2061 112 HOH TIP B . H 4 HOH 60 2062 113 HOH TIP B . H 4 HOH 61 2063 116 HOH TIP B . H 4 HOH 62 2064 117 HOH TIP B . H 4 HOH 63 2065 119 HOH TIP B . H 4 HOH 64 2066 122 HOH TIP B . H 4 HOH 65 2067 123 HOH TIP B . H 4 HOH 66 2068 124 HOH TIP B . H 4 HOH 67 2069 126 HOH TIP B . H 4 HOH 68 2070 128 HOH TIP B . H 4 HOH 69 2071 130 HOH TIP B . H 4 HOH 70 2072 131 HOH TIP B . H 4 HOH 71 2073 132 HOH TIP B . H 4 HOH 72 2074 134 HOH TIP B . H 4 HOH 73 2075 135 HOH TIP B . H 4 HOH 74 2076 139 HOH TIP B . H 4 HOH 75 2077 141 HOH TIP B . H 4 HOH 76 2078 142 HOH TIP B . H 4 HOH 77 2079 145 HOH TIP B . H 4 HOH 78 2080 146 HOH TIP B . H 4 HOH 79 2081 151 HOH TIP B . H 4 HOH 80 2082 152 HOH TIP B . H 4 HOH 81 2083 155 HOH TIP B . H 4 HOH 82 2084 156 HOH TIP B . H 4 HOH 83 2085 160 HOH TIP B . H 4 HOH 84 2086 161 HOH TIP B . H 4 HOH 85 2087 162 HOH TIP B . H 4 HOH 86 2088 163 HOH TIP B . H 4 HOH 87 2089 165 HOH TIP B . H 4 HOH 88 2090 166 HOH TIP B . H 4 HOH 89 2091 167 HOH TIP B . H 4 HOH 90 2092 168 HOH TIP B . H 4 HOH 91 2093 169 HOH TIP B . H 4 HOH 92 2094 171 HOH TIP B . H 4 HOH 93 2095 172 HOH TIP B . H 4 HOH 94 2096 174 HOH TIP B . H 4 HOH 95 2097 177 HOH TIP B . H 4 HOH 96 2098 179 HOH TIP B . H 4 HOH 97 2099 180 HOH TIP B . H 4 HOH 98 2100 181 HOH TIP B . H 4 HOH 99 2101 183 HOH TIP B . H 4 HOH 100 2102 185 HOH TIP B . H 4 HOH 101 2103 186 HOH TIP B . H 4 HOH 102 2104 187 HOH TIP B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 HKL-2000 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 MLPHARE phasing . ? 4 # _cell.entry_id 1VCD _cell.length_a 49.559 _cell.length_b 52.324 _cell.length_c 114.009 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VCD _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1VCD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.39 _exptl_crystal.density_percent_sol 48.20 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.6 _exptl_crystal_grow.pdbx_details '0.1 MHEPES, 2%(w/v) PEG 400, 1.4M ammonium sulfate, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.6' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2003-05-22 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.0 1.0 2 0.9744 1.0 3 0.9792 1.0 4 0.9798 1.0 5 0.9819 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL45XU' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL45XU _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '1.0, 0.9744, 0.9792, 0.9798, 0.9819' # _reflns.entry_id 1VCD _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20 _reflns.d_resolution_high 1.7 _reflns.number_obs 33444 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.048 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 33.1 _reflns.B_iso_Wilson_estimate 15.9 _reflns.pdbx_redundancy ? _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_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.7 _reflns_shell.d_res_low 1.76 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.28 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 7.8 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1VCD _refine.ls_number_reflns_obs 32373 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 950543.29 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.76 _refine.ls_d_res_high 1.70 _refine.ls_percent_reflns_obs 97.0 _refine.ls_R_factor_obs 0.214 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.214 _refine.ls_R_factor_R_free 0.237 _refine.ls_R_factor_R_free_error 0.004 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 3241 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 25.1 _refine.aniso_B[1][1] -7.29 _refine.aniso_B[2][2] 15.69 _refine.aniso_B[3][3] -8.40 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.493156 _refine.solvent_model_param_bsol 56.9519 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1VCD _refine_analyze.Luzzati_coordinate_error_obs 0.20 _refine_analyze.Luzzati_sigma_a_obs 0.14 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.24 _refine_analyze.Luzzati_sigma_a_free 0.16 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 2002 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 22 _refine_hist.number_atoms_solvent 183 _refine_hist.number_atoms_total 2207 _refine_hist.d_res_high 1.70 _refine_hist.d_res_low 19.76 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.005 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.3 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 23.5 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.95 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.70 _refine_ls_shell.d_res_low 1.81 _refine_ls_shell.number_reflns_R_work 4452 _refine_ls_shell.R_factor_R_work 0.258 _refine_ls_shell.percent_reflns_obs 91.8 _refine_ls_shell.R_factor_R_free 0.282 _refine_ls_shell.R_factor_R_free_error 0.012 _refine_ls_shell.percent_reflns_R_free 11.0 _refine_ls_shell.number_reflns_R_free 548 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 SO4.PARAM SO4.TOP 'X-RAY DIFFRACTION' 3 WATER_REP.PARAM WATER_REP.TOP 'X-RAY DIFFRACTION' 4 GLY.PARAM GLY.TOP 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 1VCD _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1VCD _struct.title 'Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1VCD _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text ;Nudix protein, diadenosine polyphosphate, Ap6A, Thermus thermophilus HB8, hydrolase, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics ; # 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 1 ? C N N 2 ? D N N 3 ? E N N 2 ? F N N 3 ? G N N 4 ? H N N 4 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q75UV1_THETH _struct_ref.pdbx_db_accession Q75UV1 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MELGAGGVVFNAKREVLLLRDRMGFWVFPKGHPEPGESLEEAAVREVWEETGVRAEVLLPLYPTRYVNPKGVEREVHWFL MRGEGAPRLEEGMTGAGWFSPEEARALLAFPEDLGLLEVALERLPL ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # 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 1VCD A 1 ? 126 ? Q75UV1 1 ? 126 ? 1 126 2 1 1VCD B 1 ? 126 ? Q75UV1 1 ? 126 ? 1 126 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? monomeric 1 2 author_defined_assembly ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C,D,G 2 1 B,E,F,H # _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 # 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 SER A 38 ? GLY A 52 ? SER A 38 GLY A 52 1 ? 15 HELX_P HELX_P2 2 SER A 100 ? LEU A 108 ? SER A 100 LEU A 108 1 ? 9 HELX_P HELX_P3 3 PHE A 110 ? LEU A 124 ? PHE A 110 LEU A 124 1 ? 15 HELX_P HELX_P4 4 SER B 38 ? GLY B 52 ? SER B 38 GLY B 52 1 ? 15 HELX_P HELX_P5 5 SER B 100 ? LEU B 108 ? SER B 100 LEU B 108 1 ? 9 HELX_P HELX_P6 6 PHE B 110 ? LEU B 124 ? PHE B 110 LEU B 124 1 ? 15 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 3 ? C ? 4 ? D ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? parallel A 3 4 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? parallel C 3 4 ? anti-parallel D 1 2 ? anti-parallel D 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 LYS A 30 ? GLY A 31 ? LYS A 30 GLY A 31 A 2 GLU A 2 ? PHE A 10 ? GLU A 2 PHE A 10 A 3 GLU A 73 ? GLU A 84 ? GLU A 73 GLU A 84 A 4 ARG A 54 ? VAL A 67 ? ARG A 54 VAL A 67 B 1 TRP A 26 ? VAL A 27 ? TRP A 26 VAL A 27 B 2 VAL A 16 ? ARG A 20 ? VAL A 16 ARG A 20 B 3 GLY A 95 ? PHE A 99 ? GLY A 95 PHE A 99 C 1 LYS B 30 ? GLY B 31 ? LYS B 30 GLY B 31 C 2 GLU B 2 ? PHE B 10 ? GLU B 2 PHE B 10 C 3 GLU B 73 ? ARG B 82 ? GLU B 73 ARG B 82 C 4 GLU B 56 ? VAL B 67 ? GLU B 56 VAL B 67 D 1 TRP B 26 ? VAL B 27 ? TRP B 26 VAL B 27 D 2 VAL B 16 ? ARG B 20 ? VAL B 16 ARG B 20 D 3 GLY B 95 ? PHE B 99 ? GLY B 95 PHE B 99 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O GLY A 31 ? O GLY A 31 N ALA A 5 ? N ALA A 5 A 2 3 N PHE A 10 ? N PHE A 10 O MET A 81 ? O MET A 81 A 3 4 O ARG A 74 ? O ARG A 74 N TYR A 66 ? N TYR A 66 B 1 2 O VAL A 27 ? O VAL A 27 N LEU A 19 ? N LEU A 19 B 2 3 N VAL A 16 ? N VAL A 16 O PHE A 99 ? O PHE A 99 C 1 2 O GLY B 31 ? O GLY B 31 N ALA B 5 ? N ALA B 5 C 2 3 N PHE B 10 ? N PHE B 10 O MET B 81 ? O MET B 81 C 3 4 O ARG B 74 ? O ARG B 74 N TYR B 66 ? N TYR B 66 D 1 2 O VAL B 27 ? O VAL B 27 N LEU B 19 ? N LEU B 19 D 2 3 N VAL B 16 ? N VAL B 16 O PHE B 99 ? O PHE B 99 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B SO4 1001 ? 8 'BINDING SITE FOR RESIDUE SO4 B 1001' AC2 Software A SO4 1002 ? 3 'BINDING SITE FOR RESIDUE SO4 A 1002' AC3 Software A GOL 2001 ? 5 'BINDING SITE FOR RESIDUE GOL A 2001' AC4 Software B GOL 2002 ? 6 'BINDING SITE FOR RESIDUE GOL B 2002' # 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 8 LYS B 30 ? LYS B 30 . ? 1_555 ? 2 AC1 8 TYR B 66 ? TYR B 66 . ? 1_555 ? 3 AC1 8 ASN B 68 ? ASN B 68 . ? 1_555 ? 4 AC1 8 ARG B 74 ? ARG B 74 . ? 1_555 ? 5 AC1 8 HOH H . ? HOH B 2016 . ? 1_555 ? 6 AC1 8 HOH H . ? HOH B 2030 . ? 1_555 ? 7 AC1 8 HOH H . ? HOH B 2045 . ? 1_555 ? 8 AC1 8 HOH H . ? HOH B 2066 . ? 1_555 ? 9 AC2 3 TYR A 66 ? TYR A 66 . ? 1_555 ? 10 AC2 3 ASN A 68 ? ASN A 68 . ? 1_555 ? 11 AC2 3 ARG A 74 ? ARG A 74 . ? 1_555 ? 12 AC3 5 ARG A 123 ? ARG A 123 . ? 1_555 ? 13 AC3 5 HOH G . ? HOH A 2074 . ? 1_555 ? 14 AC3 5 GLY B 36 ? GLY B 36 . ? 3_756 ? 15 AC3 5 GLU B 41 ? GLU B 41 . ? 3_756 ? 16 AC3 5 VAL B 67 ? VAL B 67 . ? 1_555 ? 17 AC4 6 ASP B 21 ? ASP B 21 . ? 1_555 ? 18 AC4 6 VAL B 27 ? VAL B 27 . ? 1_555 ? 19 AC4 6 PRO B 29 ? PRO B 29 . ? 1_555 ? 20 AC4 6 LYS B 30 ? LYS B 30 . ? 1_555 ? 21 AC4 6 GLU B 50 ? GLU B 50 . ? 1_555 ? 22 AC4 6 HOH H . ? HOH B 2015 . ? 1_555 ? # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 LEU A 61 ? ? -105.00 -100.10 2 1 PRO A 69 ? ? -56.58 -7.99 3 1 LEU B 61 ? ? -107.47 -111.82 # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name ? _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # 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 ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 GLU N N N N 74 GLU CA C N S 75 GLU C C N N 76 GLU O O N N 77 GLU CB C N N 78 GLU CG C N N 79 GLU CD C N N 80 GLU OE1 O N N 81 GLU OE2 O N N 82 GLU OXT O N N 83 GLU H H N N 84 GLU H2 H N N 85 GLU HA H N N 86 GLU HB2 H N N 87 GLU HB3 H N N 88 GLU HG2 H N N 89 GLU HG3 H N N 90 GLU HE2 H N N 91 GLU HXT H N N 92 GLY N N N N 93 GLY CA C N N 94 GLY C C N N 95 GLY O O N N 96 GLY OXT O N N 97 GLY H H N N 98 GLY H2 H N N 99 GLY HA2 H N N 100 GLY HA3 H N N 101 GLY HXT H N N 102 GOL C1 C N N 103 GOL O1 O N N 104 GOL C2 C N N 105 GOL O2 O N N 106 GOL C3 C N N 107 GOL O3 O N N 108 GOL H11 H N N 109 GOL H12 H N N 110 GOL HO1 H N N 111 GOL H2 H N N 112 GOL HO2 H N N 113 GOL H31 H N N 114 GOL H32 H N N 115 GOL HO3 H N N 116 HIS N N N N 117 HIS CA C N S 118 HIS C C N N 119 HIS O O N N 120 HIS CB C N N 121 HIS CG C Y N 122 HIS ND1 N Y N 123 HIS CD2 C Y N 124 HIS CE1 C Y N 125 HIS NE2 N Y N 126 HIS OXT O N N 127 HIS H H N N 128 HIS H2 H N N 129 HIS HA H N N 130 HIS HB2 H N N 131 HIS HB3 H N N 132 HIS HD1 H N N 133 HIS HD2 H N N 134 HIS HE1 H N N 135 HIS HE2 H N N 136 HIS HXT H N N 137 HOH O O N N 138 HOH H1 H N N 139 HOH H2 H N N 140 LEU N N N N 141 LEU CA C N S 142 LEU C C N N 143 LEU O O N N 144 LEU CB C N N 145 LEU CG C N N 146 LEU CD1 C N N 147 LEU CD2 C N N 148 LEU OXT O N N 149 LEU H H N N 150 LEU H2 H N N 151 LEU HA H N N 152 LEU HB2 H N N 153 LEU HB3 H N N 154 LEU HG H N N 155 LEU HD11 H N N 156 LEU HD12 H N N 157 LEU HD13 H N N 158 LEU HD21 H N N 159 LEU HD22 H N N 160 LEU HD23 H N N 161 LEU HXT H N N 162 LYS N N N N 163 LYS CA C N S 164 LYS C C N N 165 LYS O O N N 166 LYS CB C N N 167 LYS CG C N N 168 LYS CD C N N 169 LYS CE C N N 170 LYS NZ N N N 171 LYS OXT O N N 172 LYS H H N N 173 LYS H2 H N N 174 LYS HA H N N 175 LYS HB2 H N N 176 LYS HB3 H N N 177 LYS HG2 H N N 178 LYS HG3 H N N 179 LYS HD2 H N N 180 LYS HD3 H N N 181 LYS HE2 H N N 182 LYS HE3 H N N 183 LYS HZ1 H N N 184 LYS HZ2 H N N 185 LYS HZ3 H N N 186 LYS HXT H N N 187 MET N N N N 188 MET CA C N S 189 MET C C N N 190 MET O O N N 191 MET CB C N N 192 MET CG C N N 193 MET SD S N N 194 MET CE C N N 195 MET OXT O N N 196 MET H H N N 197 MET H2 H N N 198 MET HA H N N 199 MET HB2 H N N 200 MET HB3 H N N 201 MET HG2 H N N 202 MET HG3 H N N 203 MET HE1 H N N 204 MET HE2 H N N 205 MET HE3 H N N 206 MET HXT H N N 207 PHE N N N N 208 PHE CA C N S 209 PHE C C N N 210 PHE O O N N 211 PHE CB C N N 212 PHE CG C Y N 213 PHE CD1 C Y N 214 PHE CD2 C Y N 215 PHE CE1 C Y N 216 PHE CE2 C Y N 217 PHE CZ C Y N 218 PHE OXT O N N 219 PHE H H N N 220 PHE H2 H N N 221 PHE HA H N N 222 PHE HB2 H N N 223 PHE HB3 H N N 224 PHE HD1 H N N 225 PHE HD2 H N N 226 PHE HE1 H N N 227 PHE HE2 H N N 228 PHE HZ H N N 229 PHE HXT H N N 230 PRO N N N N 231 PRO CA C N S 232 PRO C C N N 233 PRO O O N N 234 PRO CB C N N 235 PRO CG C N N 236 PRO CD C N N 237 PRO OXT O N N 238 PRO H H N N 239 PRO HA H N N 240 PRO HB2 H N N 241 PRO HB3 H N N 242 PRO HG2 H N N 243 PRO HG3 H N N 244 PRO HD2 H N N 245 PRO HD3 H N N 246 PRO HXT H N N 247 SER N N N N 248 SER CA C N S 249 SER C C N N 250 SER O O N N 251 SER CB C N N 252 SER OG O N N 253 SER OXT O N N 254 SER H H N N 255 SER H2 H N N 256 SER HA H N N 257 SER HB2 H N N 258 SER HB3 H N N 259 SER HG H N N 260 SER HXT H N N 261 SO4 S S N N 262 SO4 O1 O N N 263 SO4 O2 O N N 264 SO4 O3 O N N 265 SO4 O4 O N N 266 THR N N N N 267 THR CA C N S 268 THR C C N N 269 THR O O N N 270 THR CB C N R 271 THR OG1 O N N 272 THR CG2 C N N 273 THR OXT O N N 274 THR H H N N 275 THR H2 H N N 276 THR HA H N N 277 THR HB H N N 278 THR HG1 H N N 279 THR HG21 H N N 280 THR HG22 H N N 281 THR HG23 H N N 282 THR HXT H N N 283 TRP N N N N 284 TRP CA C N S 285 TRP C C N N 286 TRP O O N N 287 TRP CB C N N 288 TRP CG C Y N 289 TRP CD1 C Y N 290 TRP CD2 C Y N 291 TRP NE1 N Y N 292 TRP CE2 C Y N 293 TRP CE3 C Y N 294 TRP CZ2 C Y N 295 TRP CZ3 C Y N 296 TRP CH2 C Y N 297 TRP OXT O N N 298 TRP H H N N 299 TRP H2 H N N 300 TRP HA H N N 301 TRP HB2 H N N 302 TRP HB3 H N N 303 TRP HD1 H N N 304 TRP HE1 H N N 305 TRP HE3 H N N 306 TRP HZ2 H N N 307 TRP HZ3 H N N 308 TRP HH2 H N N 309 TRP HXT H N N 310 TYR N N N N 311 TYR CA C N S 312 TYR C C N N 313 TYR O O N N 314 TYR CB C N N 315 TYR CG C Y N 316 TYR CD1 C Y N 317 TYR CD2 C Y N 318 TYR CE1 C Y N 319 TYR CE2 C Y N 320 TYR CZ C Y N 321 TYR OH O N N 322 TYR OXT O N N 323 TYR H H N N 324 TYR H2 H N N 325 TYR HA H N N 326 TYR HB2 H N N 327 TYR HB3 H N N 328 TYR HD1 H N N 329 TYR HD2 H N N 330 TYR HE1 H N N 331 TYR HE2 H N N 332 TYR HH H N N 333 TYR HXT H N N 334 VAL N N N N 335 VAL CA C N S 336 VAL C C N N 337 VAL O O N N 338 VAL CB C N N 339 VAL CG1 C N N 340 VAL CG2 C N N 341 VAL OXT O N N 342 VAL H H N N 343 VAL H2 H N N 344 VAL HA H N N 345 VAL HB H N N 346 VAL HG11 H N N 347 VAL HG12 H N N 348 VAL HG13 H N N 349 VAL HG21 H N N 350 VAL HG22 H N N 351 VAL HG23 H N N 352 VAL HXT H N N 353 # 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 ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 GLU N CA sing N N 70 GLU N H sing N N 71 GLU N H2 sing N N 72 GLU CA C sing N N 73 GLU CA CB sing N N 74 GLU CA HA sing N N 75 GLU C O doub N N 76 GLU C OXT sing N N 77 GLU CB CG sing N N 78 GLU CB HB2 sing N N 79 GLU CB HB3 sing N N 80 GLU CG CD sing N N 81 GLU CG HG2 sing N N 82 GLU CG HG3 sing N N 83 GLU CD OE1 doub N N 84 GLU CD OE2 sing N N 85 GLU OE2 HE2 sing N N 86 GLU OXT HXT sing N N 87 GLY N CA sing N N 88 GLY N H sing N N 89 GLY N H2 sing N N 90 GLY CA C sing N N 91 GLY CA HA2 sing N N 92 GLY CA HA3 sing N N 93 GLY C O doub N N 94 GLY C OXT sing N N 95 GLY OXT HXT sing N N 96 GOL C1 O1 sing N N 97 GOL C1 C2 sing N N 98 GOL C1 H11 sing N N 99 GOL C1 H12 sing N N 100 GOL O1 HO1 sing N N 101 GOL C2 O2 sing N N 102 GOL C2 C3 sing N N 103 GOL C2 H2 sing N N 104 GOL O2 HO2 sing N N 105 GOL C3 O3 sing N N 106 GOL C3 H31 sing N N 107 GOL C3 H32 sing N N 108 GOL O3 HO3 sing N N 109 HIS N CA sing N N 110 HIS N H sing N N 111 HIS N H2 sing N N 112 HIS CA C sing N N 113 HIS CA CB sing N N 114 HIS CA HA sing N N 115 HIS C O doub N N 116 HIS C OXT sing N N 117 HIS CB CG sing N N 118 HIS CB HB2 sing N N 119 HIS CB HB3 sing N N 120 HIS CG ND1 sing Y N 121 HIS CG CD2 doub Y N 122 HIS ND1 CE1 doub Y N 123 HIS ND1 HD1 sing N N 124 HIS CD2 NE2 sing Y N 125 HIS CD2 HD2 sing N N 126 HIS CE1 NE2 sing Y N 127 HIS CE1 HE1 sing N N 128 HIS NE2 HE2 sing N N 129 HIS OXT HXT sing N N 130 HOH O H1 sing N N 131 HOH O H2 sing N N 132 LEU N CA sing N N 133 LEU N H sing N N 134 LEU N H2 sing N N 135 LEU CA C sing N N 136 LEU CA CB sing N N 137 LEU CA HA sing N N 138 LEU C O doub N N 139 LEU C OXT sing N N 140 LEU CB CG sing N N 141 LEU CB HB2 sing N N 142 LEU CB HB3 sing N N 143 LEU CG CD1 sing N N 144 LEU CG CD2 sing N N 145 LEU CG HG sing N N 146 LEU CD1 HD11 sing N N 147 LEU CD1 HD12 sing N N 148 LEU CD1 HD13 sing N N 149 LEU CD2 HD21 sing N N 150 LEU CD2 HD22 sing N N 151 LEU CD2 HD23 sing N N 152 LEU OXT HXT sing N N 153 LYS N CA sing N N 154 LYS N H sing N N 155 LYS N H2 sing N N 156 LYS CA C sing N N 157 LYS CA CB sing N N 158 LYS CA HA sing N N 159 LYS C O doub N N 160 LYS C OXT sing N N 161 LYS CB CG sing N N 162 LYS CB HB2 sing N N 163 LYS CB HB3 sing N N 164 LYS CG CD sing N N 165 LYS CG HG2 sing N N 166 LYS CG HG3 sing N N 167 LYS CD CE sing N N 168 LYS CD HD2 sing N N 169 LYS CD HD3 sing N N 170 LYS CE NZ sing N N 171 LYS CE HE2 sing N N 172 LYS CE HE3 sing N N 173 LYS NZ HZ1 sing N N 174 LYS NZ HZ2 sing N N 175 LYS NZ HZ3 sing N N 176 LYS OXT HXT sing N N 177 MET N CA sing N N 178 MET N H sing N N 179 MET N H2 sing N N 180 MET CA C sing N N 181 MET CA CB sing N N 182 MET CA HA sing N N 183 MET C O doub N N 184 MET C OXT sing N N 185 MET CB CG sing N N 186 MET CB HB2 sing N N 187 MET CB HB3 sing N N 188 MET CG SD sing N N 189 MET CG HG2 sing N N 190 MET CG HG3 sing N N 191 MET SD CE sing N N 192 MET CE HE1 sing N N 193 MET CE HE2 sing N N 194 MET CE HE3 sing N N 195 MET OXT HXT sing N N 196 PHE N CA sing N N 197 PHE N H sing N N 198 PHE N H2 sing N N 199 PHE CA C sing N N 200 PHE CA CB sing N N 201 PHE CA HA sing N N 202 PHE C O doub N N 203 PHE C OXT sing N N 204 PHE CB CG sing N N 205 PHE CB HB2 sing N N 206 PHE CB HB3 sing N N 207 PHE CG CD1 doub Y N 208 PHE CG CD2 sing Y N 209 PHE CD1 CE1 sing Y N 210 PHE CD1 HD1 sing N N 211 PHE CD2 CE2 doub Y N 212 PHE CD2 HD2 sing N N 213 PHE CE1 CZ doub Y N 214 PHE CE1 HE1 sing N N 215 PHE CE2 CZ sing Y N 216 PHE CE2 HE2 sing N N 217 PHE CZ HZ sing N N 218 PHE OXT HXT sing N N 219 PRO N CA sing N N 220 PRO N CD sing N N 221 PRO N H sing N N 222 PRO CA C sing N N 223 PRO CA CB sing N N 224 PRO CA HA sing N N 225 PRO C O doub N N 226 PRO C OXT sing N N 227 PRO CB CG sing N N 228 PRO CB HB2 sing N N 229 PRO CB HB3 sing N N 230 PRO CG CD sing N N 231 PRO CG HG2 sing N N 232 PRO CG HG3 sing N N 233 PRO CD HD2 sing N N 234 PRO CD HD3 sing N N 235 PRO OXT HXT sing N N 236 SER N CA sing N N 237 SER N H sing N N 238 SER N H2 sing N N 239 SER CA C sing N N 240 SER CA CB sing N N 241 SER CA HA sing N N 242 SER C O doub N N 243 SER C OXT sing N N 244 SER CB OG sing N N 245 SER CB HB2 sing N N 246 SER CB HB3 sing N N 247 SER OG HG sing N N 248 SER OXT HXT sing N N 249 SO4 S O1 doub N N 250 SO4 S O2 doub N N 251 SO4 S O3 sing N N 252 SO4 S O4 sing N N 253 THR N CA sing N N 254 THR N H sing N N 255 THR N H2 sing N N 256 THR CA C sing N N 257 THR CA CB sing N N 258 THR CA HA sing N N 259 THR C O doub N N 260 THR C OXT sing N N 261 THR CB OG1 sing N N 262 THR CB CG2 sing N N 263 THR CB HB sing N N 264 THR OG1 HG1 sing N N 265 THR CG2 HG21 sing N N 266 THR CG2 HG22 sing N N 267 THR CG2 HG23 sing N N 268 THR OXT HXT sing N N 269 TRP N CA sing N N 270 TRP N H sing N N 271 TRP N H2 sing N N 272 TRP CA C sing N N 273 TRP CA CB sing N N 274 TRP CA HA sing N N 275 TRP C O doub N N 276 TRP C OXT sing N N 277 TRP CB CG sing N N 278 TRP CB HB2 sing N N 279 TRP CB HB3 sing N N 280 TRP CG CD1 doub Y N 281 TRP CG CD2 sing Y N 282 TRP CD1 NE1 sing Y N 283 TRP CD1 HD1 sing N N 284 TRP CD2 CE2 doub Y N 285 TRP CD2 CE3 sing Y N 286 TRP NE1 CE2 sing Y N 287 TRP NE1 HE1 sing N N 288 TRP CE2 CZ2 sing Y N 289 TRP CE3 CZ3 doub Y N 290 TRP CE3 HE3 sing N N 291 TRP CZ2 CH2 doub Y N 292 TRP CZ2 HZ2 sing N N 293 TRP CZ3 CH2 sing Y N 294 TRP CZ3 HZ3 sing N N 295 TRP CH2 HH2 sing N N 296 TRP OXT HXT sing N N 297 TYR N CA sing N N 298 TYR N H sing N N 299 TYR N H2 sing N N 300 TYR CA C sing N N 301 TYR CA CB sing N N 302 TYR CA HA sing N N 303 TYR C O doub N N 304 TYR C OXT sing N N 305 TYR CB CG sing N N 306 TYR CB HB2 sing N N 307 TYR CB HB3 sing N N 308 TYR CG CD1 doub Y N 309 TYR CG CD2 sing Y N 310 TYR CD1 CE1 sing Y N 311 TYR CD1 HD1 sing N N 312 TYR CD2 CE2 doub Y N 313 TYR CD2 HD2 sing N N 314 TYR CE1 CZ doub Y N 315 TYR CE1 HE1 sing N N 316 TYR CE2 CZ sing Y N 317 TYR CE2 HE2 sing N N 318 TYR CZ OH sing N N 319 TYR OH HH sing N N 320 TYR OXT HXT sing N N 321 VAL N CA sing N N 322 VAL N H sing N N 323 VAL N H2 sing N N 324 VAL CA C sing N N 325 VAL CA CB sing N N 326 VAL CA HA sing N N 327 VAL C O doub N N 328 VAL C OXT sing N N 329 VAL CB CG1 sing N N 330 VAL CB CG2 sing N N 331 VAL CB HB sing N N 332 VAL CG1 HG11 sing N N 333 VAL CG1 HG12 sing N N 334 VAL CG1 HG13 sing N N 335 VAL CG2 HG21 sing N N 336 VAL CG2 HG22 sing N N 337 VAL CG2 HG23 sing N N 338 VAL OXT HXT sing N N 339 # _atom_sites.entry_id 1VCD _atom_sites.fract_transf_matrix[1][1] .020178 _atom_sites.fract_transf_matrix[1][2] .000000 _atom_sites.fract_transf_matrix[1][3] .000000 _atom_sites.fract_transf_matrix[2][1] .000000 _atom_sites.fract_transf_matrix[2][2] .019112 _atom_sites.fract_transf_matrix[2][3] .000000 _atom_sites.fract_transf_matrix[3][1] .000000 _atom_sites.fract_transf_matrix[3][2] .000000 _atom_sites.fract_transf_matrix[3][3] .008771 _atom_sites.fract_transf_vector[1] .00000 _atom_sites.fract_transf_vector[2] .00000 _atom_sites.fract_transf_vector[3] .00000 # loop_ _atom_type.symbol C N O S # loop_