data_9C87 # _model_server_result.job_id z5aXqQt80iZgshKbOBlCyw _model_server_result.datetime_utc '2024-10-26 04:24:52' _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 9c87 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"EA","auth_seq_id":500}' # _entry.id 9C87 # _exptl.entry_id 9C87 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 9C87 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9C87 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 21-meric _pdbx_struct_assembly.oligomeric_count 21 _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 BA N N ? 6 DA N N ? 6 EA N 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 OG1 THR 90 A THR 126 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc2 V O2B ATP . A ATP 500 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc3 V O1A ATP . A ATP 500 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc4 V O3A ATP . A ATP 500 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc5 B OG1 THR 90 B THR 126 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc6 X O2B ATP . B ATP 500 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc7 X O3B ATP . B ATP 500 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc8 X O1A ATP . B ATP 500 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc9 X O3A ATP . B ATP 500 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc10 C OG1 THR 90 C THR 126 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc11 Z O2G ATP . C ATP 500 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc12 Z O2B ATP . C ATP 500 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc13 Z O3B ATP . C ATP 500 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc14 D OG1 THR 90 D THR 126 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc15 BA O1B ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc16 BA O2B ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc17 BA O1A ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc18 BA O2A ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc19 BA O3A ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 9C87 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 V 4 ATP A 1 500 500 ATP ATP . W 5 MG A 1 501 501 MG MG . X 4 ATP B 1 500 500 ATP ATP . Y 5 MG B 1 501 501 MG MG . Z 4 ATP C 1 500 500 ATP ATP . AA 5 MG C 1 501 501 MG MG . BA 6 ADP D 1 500 500 ADP ADP . CA 5 MG D 1 501 501 MG MG . DA 6 ADP E 1 501 501 ADP ADP . EA 6 ADP F 1 500 500 ADP ADP . FA 7 MTX S 1 201 201 MTX MTX . # 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 PB ADP . . . EA 6 147.399 106.759 173.245 1 204.16 ? PB ADP 500 F 1 HETATM 2 O O1B ADP . . . EA 6 148.804 106.315 172.916 1 204.16 ? O1B ADP 500 F 1 HETATM 3 O O2B ADP . . . EA 6 147.283 107.571 174.513 1 204.16 ? O2B ADP 500 F 1 HETATM 4 O O3B ADP . . . EA 6 146.631 107.321 172.073 1 204.16 ? O3B ADP 500 F 1 HETATM 5 P PA ADP . . . EA 6 147.125 104.483 174.829 1 204.16 ? PA ADP 500 F 1 HETATM 6 O O1A ADP . . . EA 6 148.475 103.906 174.477 1 204.16 ? O1A ADP 500 F 1 HETATM 7 O O2A ADP . . . EA 6 146.96 105.284 176.098 1 204.16 ? O2A ADP 500 F 1 HETATM 8 O O3A ADP . . . EA 6 146.632 105.388 173.593 1 204.16 ? O3A ADP 500 F 1 HETATM 9 O O5' ADP . . . EA 6 146.055 103.279 174.848 1 204.16 ? O5' ADP 500 F 1 HETATM 10 C C5' ADP . . . EA 6 146.132 102.287 175.869 1 204.16 ? C5' ADP 500 F 1 HETATM 11 C C4' ADP . . . EA 6 145.241 101.099 175.523 1 204.16 ? C4' ADP 500 F 1 HETATM 12 O O4' ADP . . . EA 6 145.467 100.69 174.171 1 204.16 ? O4' ADP 500 F 1 HETATM 13 C C3' ADP . . . EA 6 145.525 99.907 176.424 1 204.16 ? C3' ADP 500 F 1 HETATM 14 O O3' ADP . . . EA 6 144.328 99.488 177.086 1 204.16 ? O3' ADP 500 F 1 HETATM 15 C C2' ADP . . . EA 6 146.055 98.822 175.505 1 204.16 ? C2' ADP 500 F 1 HETATM 16 O O2' ADP . . . EA 6 145.432 97.561 175.769 1 204.16 ? O2' ADP 500 F 1 HETATM 17 C C1' ADP . . . EA 6 145.746 99.289 174.088 1 204.16 ? C1' ADP 500 F 1 HETATM 18 N N9 ADP . . . EA 6 146.886 99.069 173.16 1 204.16 ? N9 ADP 500 F 1 HETATM 19 C C8 ADP . . . EA 6 147.373 99.992 172.307 1 204.16 ? C8 ADP 500 F 1 HETATM 20 N N7 ADP . . . EA 6 148.405 99.486 171.586 1 204.16 ? N7 ADP 500 F 1 HETATM 21 C C5 ADP . . . EA 6 148.589 98.213 171.973 1 204.16 ? C5 ADP 500 F 1 HETATM 22 C C6 ADP . . . EA 6 149.511 97.114 171.611 1 204.16 ? C6 ADP 500 F 1 HETATM 23 N N6 ADP . . . EA 6 150.464 97.292 170.666 1 204.16 ? N6 ADP 500 F 1 HETATM 24 N N1 ADP . . . EA 6 149.366 95.934 172.253 1 204.16 ? N1 ADP 500 F 1 HETATM 25 C C2 ADP . . . EA 6 148.422 95.744 173.195 1 204.16 ? C2 ADP 500 F 1 HETATM 26 N N3 ADP . . . EA 6 147.554 96.704 173.567 1 204.16 ? N3 ADP 500 F 1 HETATM 27 C C4 ADP . . . EA 6 147.579 97.936 173.002 1 204.16 ? C4 ADP 500 F 1 HETATM 28 H "H5'1" ADP . . . EA 6 145.819 102.715 176.823 1 204.16 ? "H5'1" ADP 500 F 1 HETATM 29 H "H5'2" ADP . . . EA 6 147.168 101.956 175.969 1 204.16 ? "H5'2" ADP 500 F 1 HETATM 30 H H4' ADP . . . EA 6 144.191 101.396 175.652 1 204.16 ? H4' ADP 500 F 1 HETATM 31 H H3' ADP . . . EA 6 146.297 100.171 177.16 1 204.16 ? H3' ADP 500 F 1 HETATM 32 H HO3' ADP . . . EA 6 144.545 98.85 177.78 1 204.16 ? HO3' ADP 500 F 1 HETATM 33 H H2' ADP . . . EA 6 147.142 98.751 175.649 1 204.16 ? H2' ADP 500 F 1 HETATM 34 H HO2' ADP . . . EA 6 145.744 97.216 176.617 1 204.16 ? HO2' ADP 500 F 1 HETATM 35 H H1' ADP . . . EA 6 144.858 98.752 173.725 1 204.16 ? H1' ADP 500 F 1 HETATM 36 H H8 ADP . . . EA 6 146.998 101.004 172.21 1 204.16 ? H8 ADP 500 F 1 HETATM 37 H HN61 ADP . . . EA 6 150.553 98.184 170.2 1 204.16 ? HN61 ADP 500 F 1 HETATM 38 H HN62 ADP . . . EA 6 151.087 96.535 170.429 1 204.16 ? HN62 ADP 500 F 1 HETATM 39 H H2 ADP . . . EA 6 148.357 94.775 173.673 1 204.16 ? H2 ADP 500 F 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 252 _model_server_stats.query_time_ms 445 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #