data_2GKD # _entry.id 2GKD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2GKD pdb_00002gkd 10.2210/pdb2gkd/pdb RCSB RCSB037226 ? ? WWPDB D_1000037226 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type TargetDB GO.79751 . unspecified PDB 1ZXF 'Solution Structure of CalC' unspecified PDB 2GKC 'Structure of CalC-Calicheamicin' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2GKD _pdbx_database_status.recvd_initial_deposition_date 2006-04-01 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _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_ _audit_author.name _audit_author.pdbx_ordinal 'Singh, S.' 1 'Thorson, J.S.' 2 # _citation.id primary _citation.title 'Structural insight into the self-sacrifice mechanism of enediyne resistance.' _citation.journal_abbrev 'Acs Chem.Biol.' _citation.journal_volume 1 _citation.page_first 451 _citation.page_last 460 _citation.year 2006 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1554-8929 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17168523 _citation.pdbx_database_id_DOI 10.1021/cb6002898 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Singh, S.' 1 ? primary 'Hager, M.H.' 2 ? primary 'Zhang, C.' 3 ? primary 'Griffith, B.R.' 4 ? primary 'Lee, M.S.' 5 ? primary 'Hallenga, K.' 6 ? primary 'Markley, J.L.' 7 ? primary 'Thorson, J.S.' 8 ? # 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(*GP*CP*AP*TP*AP*TP*GP*AP*TP*AP*G)-3'" 3397.247 1 ? ? ? ? 2 polymer syn "5'-D(*CP*TP*AP*TP*CP*AP*TP*AP*TP*GP*C)-3'" 3308.185 1 ? ? ? ? 3 polymer man CalC 17915.072 1 ? ? ? ? # 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 '(DG)(DC)(DA)(DT)(DA)(DT)(DG)(DA)(DT)(DA)(DG)' GCATATGATAG B ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DA)(DT)(DC)(DA)(DT)(DA)(DT)(DG)(DC)' CTATCATATGC C ? 3 'polypeptide(L)' no no ;NYDPFVRHSVTVKADRKTAFKTFLEGFPEWWPNNFRTTKVGAPLGVDKKGGRWYEIDEQGEEHTFGLIRKVDEPDTLVIG WRLNGFGRIDPDNSSEFTVTFVADGQKKTRVDVEHTHFDRMGTKHAKRVRNGMDKGWPTILQSFQDKIDEEGAKK ; ;NYDPFVRHSVTVKADRKTAFKTFLEGFPEWWPNNFRTTKVGAPLGVDKKGGRWYEIDEQGEEHTFGLIRKVDEPDTLVIG WRLNGFGRIDPDNSSEFTVTFVADGQKKTRVDVEHTHFDRMGTKHAKRVRNGMDKGWPTILQSFQDKIDEEGAKK ; A ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DA n 1 4 DT n 1 5 DA n 1 6 DT n 1 7 DG n 1 8 DA n 1 9 DT n 1 10 DA n 1 11 DG n 2 1 DC n 2 2 DT n 2 3 DA n 2 4 DT n 2 5 DC n 2 6 DA n 2 7 DT n 2 8 DA n 2 9 DT n 2 10 DG n 2 11 DC n 3 1 ASN n 3 2 TYR n 3 3 ASP n 3 4 PRO n 3 5 PHE n 3 6 VAL n 3 7 ARG n 3 8 HIS n 3 9 SER n 3 10 VAL n 3 11 THR n 3 12 VAL n 3 13 LYS n 3 14 ALA n 3 15 ASP n 3 16 ARG n 3 17 LYS n 3 18 THR n 3 19 ALA n 3 20 PHE n 3 21 LYS n 3 22 THR n 3 23 PHE n 3 24 LEU n 3 25 GLU n 3 26 GLY n 3 27 PHE n 3 28 PRO n 3 29 GLU n 3 30 TRP n 3 31 TRP n 3 32 PRO n 3 33 ASN n 3 34 ASN n 3 35 PHE n 3 36 ARG n 3 37 THR n 3 38 THR n 3 39 LYS n 3 40 VAL n 3 41 GLY n 3 42 ALA n 3 43 PRO n 3 44 LEU n 3 45 GLY n 3 46 VAL n 3 47 ASP n 3 48 LYS n 3 49 LYS n 3 50 GLY n 3 51 GLY n 3 52 ARG n 3 53 TRP n 3 54 TYR n 3 55 GLU n 3 56 ILE n 3 57 ASP n 3 58 GLU n 3 59 GLN n 3 60 GLY n 3 61 GLU n 3 62 GLU n 3 63 HIS n 3 64 THR n 3 65 PHE n 3 66 GLY n 3 67 LEU n 3 68 ILE n 3 69 ARG n 3 70 LYS n 3 71 VAL n 3 72 ASP n 3 73 GLU n 3 74 PRO n 3 75 ASP n 3 76 THR n 3 77 LEU n 3 78 VAL n 3 79 ILE n 3 80 GLY n 3 81 TRP n 3 82 ARG n 3 83 LEU n 3 84 ASN n 3 85 GLY n 3 86 PHE n 3 87 GLY n 3 88 ARG n 3 89 ILE n 3 90 ASP n 3 91 PRO n 3 92 ASP n 3 93 ASN n 3 94 SER n 3 95 SER n 3 96 GLU n 3 97 PHE n 3 98 THR n 3 99 VAL n 3 100 THR n 3 101 PHE n 3 102 VAL n 3 103 ALA n 3 104 ASP n 3 105 GLY n 3 106 GLN n 3 107 LYS n 3 108 LYS n 3 109 THR n 3 110 ARG n 3 111 VAL n 3 112 ASP n 3 113 VAL n 3 114 GLU n 3 115 HIS n 3 116 THR n 3 117 HIS n 3 118 PHE n 3 119 ASP n 3 120 ARG n 3 121 MET n 3 122 GLY n 3 123 THR n 3 124 LYS n 3 125 HIS n 3 126 ALA n 3 127 LYS n 3 128 ARG n 3 129 VAL n 3 130 ARG n 3 131 ASN n 3 132 GLY n 3 133 MET n 3 134 ASP n 3 135 LYS n 3 136 GLY n 3 137 TRP n 3 138 PRO n 3 139 THR n 3 140 ILE n 3 141 LEU n 3 142 GLN n 3 143 SER n 3 144 PHE n 3 145 GLN n 3 146 ASP n 3 147 LYS n 3 148 ILE n 3 149 ASP n 3 150 GLU n 3 151 GLU n 3 152 GLY n 3 153 ALA n 3 154 LYS n 3 155 LYS 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 ? _entity_src_gen.gene_src_genus Micromonospora _entity_src_gen.pdbx_gene_src_gene ? _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 'Micromonospora echinospora' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1877 _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 Escherichia _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 ? _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 ? _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_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 UNP Q8KNF0_MICEC Q8KNF0 3 27 ? ? 2 PDB 2GKD 2GKD 1 ? ? ? 3 PDB 2GKD 2GKD 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 2GKD A 1 ? 155 ? Q8KNF0 27 ? 181 ? 1 155 2 2 2GKD B 1 ? 11 ? 2GKD 1 ? 11 ? 1 11 3 3 2GKD C 1 ? 11 ? 2GKD 12 ? 22 ? 12 22 # 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 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 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 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 # _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.type HSQC _pdbx_nmr_exptl.solution_id 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 303 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength '150 mM NaCl' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents 'U-15N, CalC, 50mM phosphate buffer, 150 mM NaCL' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.type ? # _pdbx_nmr_refine.entry_id 2GKD _pdbx_nmr_refine.method 'simulated annealing, molecular dynamics, Docking' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2GKD _pdbx_nmr_details.text 'NMR chemical shift perturbation information was used for docking.' # _pdbx_nmr_ensemble.entry_id 2GKD _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 2GKD _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'fewest violations' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement CNS 1.2 'Brunger A.T.' 1 refinement HADDOCK 1.1 'Bonvin, AMJJ' 2 # _exptl.entry_id 2GKD _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 2GKD _struct.title 'Structural insight into self-sacrifice mechanism of enediyne resistance' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2GKD _struct_keywords.pdbx_keywords TOXIN/DNA _struct_keywords.text 'START domain protein, TOXIN-DNA COMPLEX' # 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 ? # _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 ASP C 15 ? GLU C 25 ? ASP A 15 GLU A 25 1 ? 11 HELX_P HELX_P2 2 GLY C 26 ? TRP C 30 ? GLY A 26 TRP A 30 5 ? 5 HELX_P HELX_P3 3 PHE C 118 ? GLY C 122 ? PHE A 118 GLY A 122 5 ? 5 HELX_P HELX_P4 4 THR C 123 ? ARG C 130 ? THR A 123 ARG A 130 1 ? 8 HELX_P HELX_P5 5 GLY C 136 ? GLY C 152 ? GLY A 136 GLY A 152 1 ? 17 # _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 hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 11 N3 ? ? B DG 1 C DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 11 O2 ? ? B DG 1 C DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 11 N4 ? ? B DG 1 C DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 10 N1 ? ? B DC 2 C DG 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 10 O6 ? ? B DC 2 C DG 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 10 N2 ? ? B DC 2 C DG 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 9 N3 ? ? B DA 3 C DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 9 O4 ? ? B DA 3 C DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 8 N1 ? ? B DT 4 C DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 8 N6 ? ? B DT 4 C DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 7 N3 ? ? B DA 5 C DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 7 O4 ? ? B DA 5 C DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 6 N1 ? ? B DT 6 C DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 6 N6 ? ? B DT 6 C DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 5 N3 ? ? B DG 7 C DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 5 O2 ? ? B DG 7 C DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 5 N4 ? ? B DG 7 C DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 4 N3 ? ? B DA 8 C DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 4 O4 ? ? B DA 8 C DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 3 N1 ? ? B DT 9 C DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 3 N6 ? ? B DT 9 C DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 10 N1 ? ? ? 1_555 B DT 2 N3 ? ? B DA 10 C DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 2 O4 ? ? B DA 10 C DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 1 N3 ? ? B DG 11 C DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 1 O2 ? ? B DG 11 C DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 1 N4 ? ? B DG 11 C DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 6 _struct_sheet.details ? # 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 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? 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 VAL C 6 ? VAL C 12 ? VAL A 6 VAL A 12 A 2 LYS C 108 ? HIS C 115 ? LYS A 108 HIS A 115 A 3 PHE C 97 ? ASP C 104 ? PHE A 97 ASP A 104 A 4 THR C 76 ? GLY C 80 ? THR A 76 GLY A 80 A 5 GLY C 60 ? ASP C 72 ? GLY A 60 ASP A 72 A 6 ARG C 52 ? ASP C 57 ? ARG A 52 ASP A 57 # 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 N VAL C 12 ? N VAL A 12 O THR C 109 ? O THR A 109 A 2 3 O LYS C 108 ? O LYS A 108 N ASP C 104 ? N ASP A 104 A 3 4 O VAL C 99 ? O VAL A 99 N LEU C 77 ? N LEU A 77 A 4 5 O VAL C 78 ? O VAL A 78 N ARG C 69 ? N ARG A 69 A 5 6 O GLY C 66 ? O GLY A 66 N TRP C 53 ? N TRP A 53 # _database_PDB_matrix.entry_id 2GKD _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 # _atom_sites.entry_id 2GKD _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P S # 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 DG 1 1 1 DG G B . n A 1 2 DC 2 2 2 DC C B . n A 1 3 DA 3 3 3 DA A B . n A 1 4 DT 4 4 4 DT T B . n A 1 5 DA 5 5 5 DA A B . n A 1 6 DT 6 6 6 DT T B . n A 1 7 DG 7 7 7 DG G B . n A 1 8 DA 8 8 8 DA A B . n A 1 9 DT 9 9 9 DT T B . n A 1 10 DA 10 10 10 DA A B . n A 1 11 DG 11 11 11 DG G B . n B 2 1 DC 1 12 12 DC C C . n B 2 2 DT 2 13 13 DT T C . n B 2 3 DA 3 14 14 DA A C . n B 2 4 DT 4 15 15 DT T C . n B 2 5 DC 5 16 16 DC C C . n B 2 6 DA 6 17 17 DA A C . n B 2 7 DT 7 18 18 DT T C . n B 2 8 DA 8 19 19 DA A C . n B 2 9 DT 9 20 20 DT T C . n B 2 10 DG 10 21 21 DG G C . n B 2 11 DC 11 22 22 DC C C . n C 3 1 ASN 1 1 1 ASN ASN A . n C 3 2 TYR 2 2 2 TYR TYR A . n C 3 3 ASP 3 3 3 ASP ASP A . n C 3 4 PRO 4 4 4 PRO PRO A . n C 3 5 PHE 5 5 5 PHE PHE A . n C 3 6 VAL 6 6 6 VAL VAL A . n C 3 7 ARG 7 7 7 ARG ARG A . n C 3 8 HIS 8 8 8 HIS HIS A . n C 3 9 SER 9 9 9 SER SER A . n C 3 10 VAL 10 10 10 VAL VAL A . n C 3 11 THR 11 11 11 THR THR A . n C 3 12 VAL 12 12 12 VAL VAL A . n C 3 13 LYS 13 13 13 LYS LYS A . n C 3 14 ALA 14 14 14 ALA ALA A . n C 3 15 ASP 15 15 15 ASP ASP A . n C 3 16 ARG 16 16 16 ARG ARG A . n C 3 17 LYS 17 17 17 LYS LYS A . n C 3 18 THR 18 18 18 THR THR A . n C 3 19 ALA 19 19 19 ALA ALA A . n C 3 20 PHE 20 20 20 PHE PHE A . n C 3 21 LYS 21 21 21 LYS LYS A . n C 3 22 THR 22 22 22 THR THR A . n C 3 23 PHE 23 23 23 PHE PHE A . n C 3 24 LEU 24 24 24 LEU LEU A . n C 3 25 GLU 25 25 25 GLU GLU A . n C 3 26 GLY 26 26 26 GLY GLY A . n C 3 27 PHE 27 27 27 PHE PHE A . n C 3 28 PRO 28 28 28 PRO PRO A . n C 3 29 GLU 29 29 29 GLU GLU A . n C 3 30 TRP 30 30 30 TRP TRP A . n C 3 31 TRP 31 31 31 TRP TRP A . n C 3 32 PRO 32 32 32 PRO PRO A . n C 3 33 ASN 33 33 33 ASN ASN A . n C 3 34 ASN 34 34 34 ASN ASN A . n C 3 35 PHE 35 35 35 PHE PHE A . n C 3 36 ARG 36 36 36 ARG ARG A . n C 3 37 THR 37 37 37 THR THR A . n C 3 38 THR 38 38 38 THR THR A . n C 3 39 LYS 39 39 39 LYS LYS A . n C 3 40 VAL 40 40 40 VAL VAL A . n C 3 41 GLY 41 41 41 GLY GLY A . n C 3 42 ALA 42 42 42 ALA ALA A . n C 3 43 PRO 43 43 43 PRO PRO A . n C 3 44 LEU 44 44 44 LEU LEU A . n C 3 45 GLY 45 45 45 GLY GLY A . n C 3 46 VAL 46 46 46 VAL VAL A . n C 3 47 ASP 47 47 47 ASP ASP A . n C 3 48 LYS 48 48 48 LYS LYS A . n C 3 49 LYS 49 49 49 LYS LYS A . n C 3 50 GLY 50 50 50 GLY GLY A . n C 3 51 GLY 51 51 51 GLY GLY A . n C 3 52 ARG 52 52 52 ARG ARG A . n C 3 53 TRP 53 53 53 TRP TRP A . n C 3 54 TYR 54 54 54 TYR TYR A . n C 3 55 GLU 55 55 55 GLU GLU A . n C 3 56 ILE 56 56 56 ILE ILE A . n C 3 57 ASP 57 57 57 ASP ASP A . n C 3 58 GLU 58 58 58 GLU GLU A . n C 3 59 GLN 59 59 59 GLN GLN A . n C 3 60 GLY 60 60 60 GLY GLY A . n C 3 61 GLU 61 61 61 GLU GLU A . n C 3 62 GLU 62 62 62 GLU GLU A . n C 3 63 HIS 63 63 63 HIS HIS A . n C 3 64 THR 64 64 64 THR THR A . n C 3 65 PHE 65 65 65 PHE PHE A . n C 3 66 GLY 66 66 66 GLY GLY A . n C 3 67 LEU 67 67 67 LEU LEU A . n C 3 68 ILE 68 68 68 ILE ILE A . n C 3 69 ARG 69 69 69 ARG ARG A . n C 3 70 LYS 70 70 70 LYS LYS A . n C 3 71 VAL 71 71 71 VAL VAL A . n C 3 72 ASP 72 72 72 ASP ASP A . n C 3 73 GLU 73 73 73 GLU GLU A . n C 3 74 PRO 74 74 74 PRO PRO A . n C 3 75 ASP 75 75 75 ASP ASP A . n C 3 76 THR 76 76 76 THR THR A . n C 3 77 LEU 77 77 77 LEU LEU A . n C 3 78 VAL 78 78 78 VAL VAL A . n C 3 79 ILE 79 79 79 ILE ILE A . n C 3 80 GLY 80 80 80 GLY GLY A . n C 3 81 TRP 81 81 81 TRP TRP A . n C 3 82 ARG 82 82 82 ARG ARG A . n C 3 83 LEU 83 83 83 LEU LEU A . n C 3 84 ASN 84 84 84 ASN ASN A . n C 3 85 GLY 85 85 85 GLY GLY A . n C 3 86 PHE 86 86 86 PHE PHE A . n C 3 87 GLY 87 87 87 GLY GLY A . n C 3 88 ARG 88 88 88 ARG ARG A . n C 3 89 ILE 89 89 89 ILE ILE A . n C 3 90 ASP 90 90 90 ASP ASP A . n C 3 91 PRO 91 91 91 PRO PRO A . n C 3 92 ASP 92 92 92 ASP ASP A . n C 3 93 ASN 93 93 93 ASN ASN A . n C 3 94 SER 94 94 94 SER SER A . n C 3 95 SER 95 95 95 SER SER A . n C 3 96 GLU 96 96 96 GLU GLU A . n C 3 97 PHE 97 97 97 PHE PHE A . n C 3 98 THR 98 98 98 THR THR A . n C 3 99 VAL 99 99 99 VAL VAL A . n C 3 100 THR 100 100 100 THR THR A . n C 3 101 PHE 101 101 101 PHE PHE A . n C 3 102 VAL 102 102 102 VAL VAL A . n C 3 103 ALA 103 103 103 ALA ALA A . n C 3 104 ASP 104 104 104 ASP ASP A . n C 3 105 GLY 105 105 105 GLY GLY A . n C 3 106 GLN 106 106 106 GLN GLN A . n C 3 107 LYS 107 107 107 LYS LYS A . n C 3 108 LYS 108 108 108 LYS LYS A . n C 3 109 THR 109 109 109 THR THR A . n C 3 110 ARG 110 110 110 ARG ARG A . n C 3 111 VAL 111 111 111 VAL VAL A . n C 3 112 ASP 112 112 112 ASP ASP A . n C 3 113 VAL 113 113 113 VAL VAL A . n C 3 114 GLU 114 114 114 GLU GLU A . n C 3 115 HIS 115 115 115 HIS HIS A . n C 3 116 THR 116 116 116 THR THR A . n C 3 117 HIS 117 117 117 HIS HIS A . n C 3 118 PHE 118 118 118 PHE PHE A . n C 3 119 ASP 119 119 119 ASP ASP A . n C 3 120 ARG 120 120 120 ARG ARG A . n C 3 121 MET 121 121 121 MET MET A . n C 3 122 GLY 122 122 122 GLY GLY A . n C 3 123 THR 123 123 123 THR THR A . n C 3 124 LYS 124 124 124 LYS LYS A . n C 3 125 HIS 125 125 125 HIS HIS A . n C 3 126 ALA 126 126 126 ALA ALA A . n C 3 127 LYS 127 127 127 LYS LYS A . n C 3 128 ARG 128 128 128 ARG ARG A . n C 3 129 VAL 129 129 129 VAL VAL A . n C 3 130 ARG 130 130 130 ARG ARG A . n C 3 131 ASN 131 131 131 ASN ASN A . n C 3 132 GLY 132 132 132 GLY GLY A . n C 3 133 MET 133 133 133 MET MET A . n C 3 134 ASP 134 134 134 ASP ASP A . n C 3 135 LYS 135 135 135 LYS LYS A . n C 3 136 GLY 136 136 136 GLY GLY A . n C 3 137 TRP 137 137 137 TRP TRP A . n C 3 138 PRO 138 138 138 PRO PRO A . n C 3 139 THR 139 139 139 THR THR A . n C 3 140 ILE 140 140 140 ILE ILE A . n C 3 141 LEU 141 141 141 LEU LEU A . n C 3 142 GLN 142 142 142 GLN GLN A . n C 3 143 SER 143 143 143 SER SER A . n C 3 144 PHE 144 144 144 PHE PHE A . n C 3 145 GLN 145 145 145 GLN GLN A . n C 3 146 ASP 146 146 146 ASP ASP A . n C 3 147 LYS 147 147 147 LYS LYS A . n C 3 148 ILE 148 148 148 ILE ILE A . n C 3 149 ASP 149 149 149 ASP ASP A . n C 3 150 GLU 150 150 150 GLU GLU A . n C 3 151 GLU 151 151 151 GLU GLU A . n C 3 152 GLY 152 152 152 GLY GLY A . n C 3 153 ALA 153 153 153 ALA ALA A . n C 3 154 LYS 154 154 154 LYS LYS A . n C 3 155 LYS 155 155 155 LYS LYS A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _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 # 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 2006-08-22 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 # _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' 'Version format compliance' 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' database_2 2 4 'Structure model' pdbx_database_related 3 4 'Structure model' pdbx_nmr_software 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list # 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_database_related.db_name' 4 4 'Structure model' '_pdbx_nmr_software.name' # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 HD3 A LYS 39 ? ? H A VAL 40 ? ? 1.26 2 1 OE2 A GLU 55 ? ? HE2 A HIS 63 ? ? 1.55 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DA _pdbx_validate_rmsd_bond.auth_seq_id_1 10 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DA _pdbx_validate_rmsd_bond.auth_seq_id_2 10 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.372 _pdbx_validate_rmsd_bond.bond_target_value 1.419 _pdbx_validate_rmsd_bond.bond_deviation -0.047 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" B DT 4 ? ? "C4'" B DT 4 ? ? "C3'" B DT 4 ? ? 102.10 104.50 -2.40 0.40 N 2 1 "O3'" B DT 4 ? ? P B DA 5 ? ? OP2 B DA 5 ? ? 88.42 105.20 -16.78 2.20 Y 3 1 "O3'" B DT 4 ? ? P B DA 5 ? ? OP1 B DA 5 ? ? 131.32 110.50 20.82 1.10 Y 4 1 "O4'" B DA 5 ? ? "C4'" B DA 5 ? ? "C3'" B DA 5 ? ? 101.88 104.50 -2.62 0.40 N 5 1 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? N1 B DT 9 ? ? 110.54 108.30 2.24 0.30 N 6 1 "O4'" B DA 10 ? ? "C1'" B DA 10 ? ? "C2'" B DA 10 ? ? 109.80 106.80 3.00 0.50 N 7 1 "O5'" B DG 11 ? ? P B DG 11 ? ? OP1 B DG 11 ? ? 99.84 105.70 -5.86 0.90 N 8 1 "O3'" C DA 14 ? ? P C DT 15 ? ? OP1 C DT 15 ? ? 122.10 110.50 11.60 1.10 Y 9 1 N1 C DA 17 ? ? C6 C DA 17 ? ? N6 C DA 17 ? ? 122.25 118.60 3.65 0.60 N 10 1 C5 C DA 17 ? ? C6 C DA 17 ? ? N6 C DA 17 ? ? 118.29 123.70 -5.41 0.80 N # 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 ASP A 15 ? ? 141.65 165.55 2 1 TRP A 31 ? ? -142.00 21.19 3 1 PHE A 35 ? ? -74.51 46.77 4 1 LYS A 39 ? ? -146.02 -146.37 5 1 PRO A 43 ? ? -69.40 66.69 6 1 LEU A 44 ? ? -174.77 -85.71 7 1 HIS A 63 ? ? -31.41 133.60 8 1 ASP A 72 ? ? -101.64 63.50 9 1 GLU A 73 ? ? 48.27 -170.39 10 1 PRO A 74 ? ? -60.36 84.12 11 1 ASP A 75 ? ? -172.86 -70.00 12 1 ARG A 82 ? ? -177.78 149.58 13 1 LEU A 83 ? ? -138.86 -159.99 14 1 PHE A 86 ? ? -130.87 -152.54 15 1 PRO A 91 ? ? -67.41 41.57 16 1 SER A 94 ? ? 68.12 -48.44 17 1 SER A 95 ? ? 29.33 87.25 18 1 GLN A 106 ? ? 58.09 19.60 19 1 LYS A 107 ? ? -142.40 14.17 20 1 HIS A 117 ? ? -175.12 -69.45 21 1 MET A 121 ? ? -60.90 4.56 22 1 THR A 123 ? ? 82.37 -93.19 23 1 ALA A 153 ? ? -172.56 -53.55 24 1 LYS A 154 ? ? -91.52 -64.92 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DA B 10 ? ? 0.154 'SIDE CHAIN' 2 1 DA C 17 ? ? 0.060 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2GKD 'double helix' 2GKD 'b-form double helix' # 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 DG 1 1_555 B DC 11 1_555 -0.496 -0.178 0.364 20.705 4.272 -0.925 1 B_DG1:DC22_C B 1 ? C 22 ? 19 1 1 A DC 2 1_555 B DG 10 1_555 0.522 -0.334 0.041 14.133 -17.396 -4.243 2 B_DC2:DG21_C B 2 ? C 21 ? 19 1 1 A DA 3 1_555 B DT 9 1_555 0.377 -0.123 0.280 -0.880 -14.781 -6.569 3 B_DA3:DT20_C B 3 ? C 20 ? 20 1 1 A DT 4 1_555 B DA 8 1_555 0.282 -0.219 0.657 -12.722 -9.726 0.100 4 B_DT4:DA19_C B 4 ? C 19 ? 20 1 1 A DA 5 1_555 B DT 7 1_555 -0.223 -0.154 -0.041 0.438 -8.348 -4.395 5 B_DA5:DT18_C B 5 ? C 18 ? 20 1 1 A DT 6 1_555 B DA 6 1_555 -0.636 0.036 0.077 9.485 -7.845 -12.499 6 B_DT6:DA17_C B 6 ? C 17 ? 20 1 1 A DG 7 1_555 B DC 5 1_555 -0.548 -0.286 0.340 11.094 -7.603 -1.997 7 B_DG7:DC16_C B 7 ? C 16 ? 19 1 1 A DA 8 1_555 B DT 4 1_555 0.078 -0.192 -0.190 -4.375 -17.813 -3.027 8 B_DA8:DT15_C B 8 ? C 15 ? 20 1 1 A DT 9 1_555 B DA 3 1_555 0.015 -0.157 0.118 -2.732 -15.117 1.259 9 B_DT9:DA14_C B 9 ? C 14 ? 20 1 1 A DA 10 1_555 B DT 2 1_555 0.507 -0.059 -0.366 -16.894 -17.607 3.057 10 B_DA10:DT13_C B 10 ? C 13 ? 20 1 1 A DG 11 1_555 B DC 1 1_555 0.076 -0.133 -0.075 -15.223 -18.616 -1.638 11 B_DG11:DC12_C B 11 ? C 12 ? 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 DG 1 1_555 B DC 11 1_555 A DC 2 1_555 B DG 10 1_555 -0.193 -0.322 3.297 1.527 2.672 36.248 -0.888 0.522 3.255 4.285 -2.450 36.374 1 BB_DG1DC2:DG21DC22_CC B 1 ? C 22 ? B 2 ? C 21 ? 1 A DC 2 1_555 B DG 10 1_555 A DA 3 1_555 B DT 9 1_555 -0.722 -0.859 3.290 -4.323 16.415 35.576 -3.170 0.576 2.718 25.176 6.631 39.300 2 BB_DC2DA3:DT20DG21_CC B 2 ? C 21 ? B 3 ? C 20 ? 1 A DA 3 1_555 B DT 9 1_555 A DT 4 1_555 B DA 8 1_555 0.656 -1.355 3.401 -1.854 -1.326 32.006 -2.202 -1.534 3.411 -2.401 3.358 32.085 3 BB_DA3DT4:DA19DT20_CC B 3 ? C 20 ? B 4 ? C 19 ? 1 A DT 4 1_555 B DA 8 1_555 A DA 5 1_555 B DT 7 1_555 -0.192 -1.035 2.574 5.912 17.176 28.791 -3.707 0.994 1.647 30.959 -10.656 33.940 4 BB_DT4DA5:DT18DA19_CC B 4 ? C 19 ? B 5 ? C 18 ? 1 A DA 5 1_555 B DT 7 1_555 A DT 6 1_555 B DA 6 1_555 -0.600 -0.725 3.014 -3.842 6.077 26.496 -2.892 0.403 2.837 12.959 8.191 27.438 5 BB_DA5DT6:DA17DT18_CC B 5 ? C 18 ? B 6 ? C 17 ? 1 A DT 6 1_555 B DA 6 1_555 A DG 7 1_555 B DC 5 1_555 0.647 -0.666 2.897 -2.594 15.566 29.678 -3.287 -1.477 2.221 28.033 4.672 33.530 6 BB_DT6DG7:DC16DA17_CC B 6 ? C 17 ? B 7 ? C 16 ? 1 A DG 7 1_555 B DC 5 1_555 A DA 8 1_555 B DT 4 1_555 -0.008 -0.545 3.462 4.414 9.151 38.539 -1.904 0.544 3.234 13.579 -6.550 39.806 7 BB_DG7DA8:DT15DC16_CC B 7 ? C 16 ? B 8 ? C 15 ? 1 A DA 8 1_555 B DT 4 1_555 A DT 9 1_555 B DA 3 1_555 0.568 -0.857 2.983 -0.431 -2.225 32.290 -1.177 -1.089 3.026 -3.994 0.774 32.368 8 BB_DA8DT9:DA14DT15_CC B 8 ? C 15 ? B 9 ? C 14 ? 1 A DT 9 1_555 B DA 3 1_555 A DA 10 1_555 B DT 2 1_555 0.072 -1.312 3.257 8.408 19.251 33.320 -4.034 0.800 2.171 30.141 -13.165 39.230 9 BB_DT9DA10:DT13DA14_CC B 9 ? C 14 ? B 10 ? C 13 ? 1 A DA 10 1_555 B DT 2 1_555 A DG 11 1_555 B DC 1 1_555 -0.169 -0.468 3.070 -5.004 7.888 29.276 -2.320 -0.592 2.840 15.129 9.596 30.699 10 BB_DA10DG11:DC12DT13_CC B 10 ? C 13 ? B 11 ? C 12 ? #