data_8APF # _model_server_result.job_id DRiTDccjwX4AKuJQ6msv9Q _model_server_result.datetime_utc '2024-11-15 07:57:16' _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 8apf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"YB","auth_seq_id":601}' # _entry.id 8APF # _exptl.entry_id 8APF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 34 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 8APF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8APF _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 42-meric _pdbx_struct_assembly.oligomeric_count 42 _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,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB _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 # _struct_asym.details ? _struct_asym.entity_id 34 _struct_asym.id YB _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 covale ? covale1 V C AME 1 e AME 1 1_555 V N GLN 2 e GLN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 KA OG1 THR 213 A1 THR 213 1_555 RB MG MG . A1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc2 QB O2G ATP . A1 ATP 601 1_555 RB MG MG . A1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc3 QB O2B ATP . A1 ATP 601 1_555 RB MG MG . A1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc4 LA OG1 THR 213 B1 THR 213 1_555 TB MG MG . B1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc5 SB O2G ATP . B1 ATP 601 1_555 TB MG MG . B1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.871 ? metalc ? metalc6 SB O2B ATP . B1 ATP 601 1_555 TB MG MG . B1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc7 MA OG1 THR 213 C1 THR 213 1_555 VB MG MG . C1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc8 UB O2G ATP . C1 ATP 601 1_555 VB MG MG . C1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc9 UB O2B ATP . C1 ATP 601 1_555 VB MG MG . C1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc10 NA OG1 THR 190 D1 THR 190 1_555 XB MG MG . D1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc11 NA OE2 GLU 215 D1 GLU 215 1_555 XB MG MG . D1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc12 WB O2G ATP . D1 ATP 601 1_555 XB MG MG . D1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc13 WB O2B ATP . D1 ATP 601 1_555 XB MG MG . D1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc14 OA OG1 THR 190 E1 THR 190 1_555 ZB MG MG . E1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc15 YB O3B ADP . E1 ADP 601 1_555 ZB MG MG . E1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? # _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 ? # _atom_sites.entry_id 8APF _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 QA 26 CDL L 1 101 12 CDL CDL . RA 26 CDL M 1 201 1 CDL CDL . SA 27 PEE M 1 202 2 PEE PEE . TA 26 CDL c 1 201 3 CDL CDL . UA 26 CDL e 1 401 2 CDL CDL . VA 26 CDL e 1 402 5 CDL CDL . WA 26 CDL e 1 403 7 CDL CDL . XA 26 CDL e 1 404 10 CDL CDL . YA 26 CDL e 1 405 11 CDL CDL . ZA 28 LMT e 1 406 1 LMT LMT . AB 29 Q7G e 1 407 2 Q7G GD0 . BB 26 CDL f 1 201 9 CDL CDL . CB 27 PEE f 1 202 1 PEE PEE . DB 30 PC1 f 1 203 2 PC1 PC1 . EB 30 PC1 i 1 201 4 PC1 PC1 . FB 26 CDL j 1 201 4 CDL CDL . GB 30 PC1 j 1 202 3 PC1 PC1 . HB 28 LMT j 1 203 2 LMT LMT . IB 26 CDL l 1 101 12 CDL CDL . JB 27 PEE m 1 201 2 PEE PEE . KB 26 CDL m 1 202 1 CDL CDL . LB 29 Q7G n 1 201 1 Q7G GD0 . MB 30 PC1 p 1 201 1 PC1 PC1 . NB 26 CDL q 1 101 6 CDL CDL . OB 26 CDL q 1 102 8 CDL CDL . PB 31 UTP G1 1 401 1 UTP UTP . QB 32 ATP A1 1 601 5 ATP ATP . RB 33 MG A1 1 602 6 MG MG . SB 32 ATP B1 1 601 1 ATP ATP . TB 33 MG B1 1 602 2 MG MG . UB 32 ATP C1 1 601 3 ATP ATP . VB 33 MG C1 1 602 4 MG MG . WB 32 ATP D1 1 601 7 ATP ATP . XB 33 MG D1 1 602 8 MG MG . YB 34 ADP E1 1 601 1 ADP ADP . ZB 33 MG E1 1 602 2 MG MG . # 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 . . . YB 34 342.773 168.297 273.575 1 109.7 ? PB ADP 601 E1 1 HETATM 2 O O1B ADP . . . YB 34 343.522 169.389 272.805 1 109.7 ? O1B ADP 601 E1 1 HETATM 3 O O2B ADP . . . YB 34 341.785 168.957 274.541 1 109.7 ? O2B ADP 601 E1 1 HETATM 4 O O3B ADP . . . YB 34 343.675 167.309 274.23 1 109.7 ? O3B ADP 601 E1 1 HETATM 5 P PA ADP . . . YB 34 341.355 166.094 272.283 1 109.7 ? PA ADP 601 E1 1 HETATM 6 O O1A ADP . . . YB 34 342.238 165.349 271.365 1 109.7 ? O1A ADP 601 E1 1 HETATM 7 O O2A ADP . . . YB 34 341.216 165.485 273.676 1 109.7 ? O2A ADP 601 E1 1 HETATM 8 O O3A ADP . . . YB 34 341.852 167.594 272.478 1 109.7 ? O3A ADP 601 E1 1 HETATM 9 O O5' ADP . . . YB 34 339.861 166.233 271.695 1 109.7 ? O5' ADP 601 E1 1 HETATM 10 C C5' ADP . . . YB 34 339.141 165.114 271.137 1 109.7 ? C5' ADP 601 E1 1 HETATM 11 C C4' ADP . . . YB 34 337.874 165.618 270.494 1 109.7 ? C4' ADP 601 E1 1 HETATM 12 O O4' ADP . . . YB 34 338.199 166.644 269.528 1 109.7 ? O4' ADP 601 E1 1 HETATM 13 C C3' ADP . . . YB 34 337.076 164.56 269.733 1 109.7 ? C3' ADP 601 E1 1 HETATM 14 O O3' ADP . . . YB 34 336.071 163.987 270.562 1 109.7 ? O3' ADP 601 E1 1 HETATM 15 C C2' ADP . . . YB 34 336.466 165.362 268.582 1 109.7 ? C2' ADP 601 E1 1 HETATM 16 O O2' ADP . . . YB 34 335.287 166.051 268.985 1 109.7 ? O2' ADP 601 E1 1 HETATM 17 C C1' ADP . . . YB 34 337.588 166.355 268.285 1 109.7 ? C1' ADP 601 E1 1 HETATM 18 N N9 ADP . . . YB 34 338.615 165.847 267.382 1 109.7 ? N9 ADP 601 E1 1 HETATM 19 C C8 ADP . . . YB 34 339.966 165.821 267.607 1 109.7 ? C8 ADP 601 E1 1 HETATM 20 N N7 ADP . . . YB 34 340.664 165.312 266.622 1 109.7 ? N7 ADP 601 E1 1 HETATM 21 C C5 ADP . . . YB 34 339.703 164.979 265.678 1 109.7 ? C5 ADP 601 E1 1 HETATM 22 C C6 ADP . . . YB 34 339.792 164.4 264.398 1 109.7 ? C6 ADP 601 E1 1 HETATM 23 N N6 ADP . . . YB 34 340.942 164.035 263.823 1 109.7 ? N6 ADP 601 E1 1 HETATM 24 N N1 ADP . . . YB 34 338.642 164.206 263.716 1 109.7 ? N1 ADP 601 E1 1 HETATM 25 C C2 ADP . . . YB 34 337.489 164.57 264.284 1 109.7 ? C2 ADP 601 E1 1 HETATM 26 N N3 ADP . . . YB 34 337.283 165.124 265.481 1 109.7 ? N3 ADP 601 E1 1 HETATM 27 C C4 ADP . . . YB 34 338.436 165.303 266.133 1 109.7 ? C4 ADP 601 E1 1 HETATM 28 H "H5'1" ADP . . . YB 34 338.936 164.369 271.904 1 109.7 ? "H5'1" ADP 601 E1 1 HETATM 29 H "H5'2" ADP . . . YB 34 339.825 164.663 270.42 1 109.7 ? "H5'2" ADP 601 E1 1 HETATM 30 H H4' ADP . . . YB 34 337.245 166.13 271.22 1 109.7 ? H4' ADP 601 E1 1 HETATM 31 H H3' ADP . . . YB 34 337.719 163.764 269.36 1 109.7 ? H3' ADP 601 E1 1 HETATM 32 H HO3' ADP . . . YB 34 335.59 163.314 270.013 1 109.7 ? HO3' ADP 601 E1 1 HETATM 33 H H2' ADP . . . YB 34 336.23 164.704 267.748 1 109.7 ? H2' ADP 601 E1 1 HETATM 34 H HO2' ADP . . . YB 34 334.622 165.362 269.25 1 109.7 ? HO2' ADP 601 E1 1 HETATM 35 H H1' ADP . . . YB 34 337.216 167.29 267.869 1 109.7 ? H1' ADP 601 E1 1 HETATM 36 H H8 ADP . . . YB 34 340.411 166.193 268.529 1 109.7 ? H8 ADP 601 E1 1 HETATM 37 H HN61 ADP . . . YB 34 341.836 164.187 264.279 1 109.7 ? HN61 ADP 601 E1 1 HETATM 38 H HN62 ADP . . . YB 34 340.939 163.593 262.909 1 109.7 ? HN62 ADP 601 E1 1 HETATM 39 H H2 ADP . . . YB 34 336.6 164.383 263.683 1 109.7 ? H2 ADP 601 E1 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 162 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 39 #