data_4KB6 # _model_server_result.job_id WFP0o7beu6DsFyB06ur0WQ _model_server_result.datetime_utc '2024-12-24 16:54:06' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4kb6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":503}' # _entry.id 4KB6 # _exptl.entry_id 4KB6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 4KB6 _cell.length_a 86.28 _cell.length_b 111.89 _cell.length_c 117.78 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KB6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OG SER 57 A SER 188 1_555 G MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc2 A OE1 GLN 69 A GLN 200 1_555 G MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc3 A OD1 ASN 71 A ASN 202 1_555 G MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc4 A SG CYS 242 A CYS 373 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc5 A SG CYS 243 A CYS 374 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc6 A SG CYS 250 A CYS 381 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc7 F O3B ATP . A ATP 503 1_555 G MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc8 F O3A ATP . A ATP 503 1_555 G MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? hydrog 'DC-DG PAIR' hydrog1 B N4 DC 1 B DC 1 1_555 C O6 DG 14 C DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N1 DG 2 B DG 2 1_555 C N3 DC 13 C DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N2 DG 2 B DG 2 1_555 C O2 DC 13 C DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B O6 DG 2 B DG 2 1_555 C N4 DC 13 C DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DG MISPAIR' hydrog5 B N6 DA 3 B DA 3 1_555 C O6 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DA 3 B DA 3 1_555 C N3 DT 12 C DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 DA 3 B DA 3 1_555 C O4 DT 12 C DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 4 B DC 4 1_555 C N1 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 4 B DC 4 1_555 C O6 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 4 B DC 4 1_555 C N2 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DG 5 B DG 5 1_555 C N3 DC 10 C DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N2 DG 5 B DG 5 1_555 C O2 DC 10 C DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O6 DG 5 B DG 5 1_555 C N4 DC 10 C DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DC 6 B DC 6 1_555 C N1 DG 9 C DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 DC 6 B DC 6 1_555 C O6 DG 9 C DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 DC 6 B DC 6 1_555 C N2 DG 9 C DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DT 7 B DT 7 1_555 C N1 DA 8 C DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O4 DT 7 B DT 7 1_555 C N6 DA 8 C DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DA 8 B DA 8 1_555 C N3 DT 7 C DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N6 DA 8 B DA 8 1_555 C O4 DT 7 C DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog21 B N1 DG 9 B DG 9 1_555 C N3 DC 6 C DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog22 B N3 DC 10 B DC 10 1_555 C N2 DG 5 C DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog23 B O2 DC 10 B DC 10 1_555 C N1 DG 5 C DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N1 DG 11 B DG 11 1_555 C N3 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N2 DG 11 B DG 11 1_555 C O2 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O6 DG 11 B DG 11 1_555 C N4 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N3 DT 12 B DT 12 1_555 C N1 DA 3 C DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O4 DT 12 B DT 12 1_555 C N6 DA 3 C DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog29 B O2 DC 13 B DC 13 1_555 C N1 DG 2 C DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 4KB6 _atom_sites.fract_transf_matrix[1][1] 0.01159 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008937 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.00849 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code D 3 ZN A 1 501 1 ZN ZN . E 4 GTP A 1 502 1 GTP GTP . F 5 ATP A 1 503 1 ATP ATP . G 6 MG A 1 504 1 MG MG . H 7 HOH A 1 601 1 HOH HOH . H 7 HOH A 2 602 2 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PG ATP . . . F 5 -17.102 -25.42 -9.635 1 165.04 ? PG ATP 503 A 1 HETATM 2 O O1G ATP . . . F 5 -16.151 -24.467 -9.022 1 164.61 ? O1G ATP 503 A 1 HETATM 3 O O2G ATP . . . F 5 -18.159 -24.565 -10.23 1 161.53 ? O2G ATP 503 A 1 HETATM 4 O O3G ATP . . . F 5 -17.753 -26.067 -8.476 1 167.9 ? O3G ATP 503 A 1 HETATM 5 P PB ATP . . . F 5 -17.062 -26.997 -11.964 1 181.19 ? PB ATP 503 A 1 HETATM 6 O O1B ATP . . . F 5 -18.011 -26.047 -12.586 1 181.42 ? O1B ATP 503 A 1 HETATM 7 O O2B ATP . . . F 5 -16.037 -27.107 -13.026 1 178.68 ? O2B ATP 503 A 1 HETATM 8 O O3B ATP . . . F 5 -16.41 -26.431 -10.639 1 232.36 ? O3B ATP 503 A 1 HETATM 9 P PA ATP . . . F 5 -19.154 -28.832 -12.306 1 135.68 ? PA ATP 503 A 1 HETATM 10 O O1A ATP . . . F 5 -20.228 -27.844 -12.048 1 140.52 ? O1A ATP 503 A 1 HETATM 11 O O2A ATP . . . F 5 -19.715 -30.04 -11.643 1 139.02 ? O2A ATP 503 A 1 HETATM 12 O O3A ATP . . . F 5 -17.762 -28.399 -11.658 1 206.68 ? O3A ATP 503 A 1 HETATM 13 O O5' ATP . . . F 5 -18.904 -29.083 -13.857 1 161.19 ? O5' ATP 503 A 1 HETATM 14 C C5' ATP . . . F 5 -17.537 -29.276 -14.26 1 164.57 ? C5' ATP 503 A 1 HETATM 15 C C4' ATP . . . F 5 -17.44 -29.659 -15.77 1 115.77 ? C4' ATP 503 A 1 HETATM 16 O O4' ATP . . . F 5 -18.494 -30.249 -16.137 1 112.02 ? O4' ATP 503 A 1 HETATM 17 C C3' ATP . . . F 5 -17.436 -28.415 -16.672 1 116.32 ? C3' ATP 503 A 1 HETATM 18 O O3' ATP . . . F 5 -16.195 -28.12 -17.071 1 116.92 ? O3' ATP 503 A 1 HETATM 19 C C2' ATP . . . F 5 -18.324 -28.895 -17.865 1 108.98 ? C2' ATP 503 A 1 HETATM 20 O O2' ATP . . . F 5 -17.579 -29.39 -18.857 1 117.85 ? O2' ATP 503 A 1 HETATM 21 C C1' ATP . . . F 5 -19.135 -30.022 -17.213 1 106.22 ? C1' ATP 503 A 1 HETATM 22 N N9 ATP . . . F 5 -20.492 -29.622 -16.913 1 104.34 ? N9 ATP 503 A 1 HETATM 23 C C8 ATP . . . F 5 -21.274 -29.285 -15.537 1 113.62 ? C8 ATP 503 A 1 HETATM 24 N N7 ATP . . . F 5 -22.567 -28.966 -15.787 1 111.19 ? N7 ATP 503 A 1 HETATM 25 C C5 ATP . . . F 5 -22.819 -29.013 -16.927 1 109.94 ? C5 ATP 503 A 1 HETATM 26 C C6 ATP . . . F 5 -24.026 -28.767 -17.683 1 116.34 ? C6 ATP 503 A 1 HETATM 27 N N6 ATP . . . F 5 -25.217 -28.383 -17.022 1 120.33 ? N6 ATP 503 A 1 HETATM 28 N N1 ATP . . . F 5 -23.982 -28.896 -18.85 1 115.16 ? N1 ATP 503 A 1 HETATM 29 C C2 ATP . . . F 5 -23.184 -29.178 -19.568 1 107.69 ? C2 ATP 503 A 1 HETATM 30 N N3 ATP . . . F 5 -22.034 -29.445 -19.195 1 101.33 ? N3 ATP 503 A 1 HETATM 31 C C4 ATP . . . F 5 -21.705 -29.391 -17.761 1 103.6 ? C4 ATP 503 A 1 HETATM 32 H HO3' ATP . . . F 5 -16.231 -27.584 -17.785 1 140.3 ? HO3' ATP 503 A 1 HETATM 33 H HO2' ATP . . . F 5 -16.93 -28.802 -19.068 1 141.42 ? HO2' ATP 503 A 1 HETATM 34 H HN61 ATP . . . F 5 -25.85 -27.902 -17.467 1 144.4 ? HN61 ATP 503 A 1 HETATM 35 H HN62 ATP . . . F 5 -25.351 -28.616 -16.157 1 144.4 ? HN62 ATP 503 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 500 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 35 #