data_8C1D # _model_server_result.job_id 5ZZthBBWQ79umzTrxKcN-Q _model_server_result.datetime_utc '2024-10-10 07:25:14' _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 8c1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 8C1D # _exptl.entry_id 8C1D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 120 _cell.entry_id 8C1D _cell.length_a 81.341 _cell.length_b 81.341 _cell.length_c 171.531 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8C1D _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_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 _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 3 _struct_asym.id C _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 OD2 ASP 151 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc2 A OD1 ASP 151 A ASP 274 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc3 A OD2 ASP 151 A ASP 274 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc4 C O1B ADP . A ADP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc5 C O1A ADP . A ADP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc6 C O3B ADP . A ADP 402 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc7 D MG MG . A MG 403 1_555 P O HOH . A HOH 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc8 D MG MG . A MG 403 1_555 P O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc9 E MG MG . A MG 404 1_555 F O2 T5L . A T5L 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc10 E MG MG . A MG 404 1_555 P O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc11 E MG MG . A MG 404 1_555 P O HOH . A HOH 532 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? # _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 7 n n PB O2B ADP sing 8 n n PB O3B ADP sing 9 n n PB O3A ADP sing 10 n n O2B HOB2 ADP sing 11 n n O3B HOB3 ADP sing 12 n n PA O1A ADP doub 13 n n PA O2A ADP sing 14 n n PA O3A ADP sing 15 n n PA O5' ADP sing 16 n n O2A HOA2 ADP sing 17 n n O5' C5' ADP sing 18 n n C5' C4' ADP sing 19 n n C5' "H5'1" ADP sing 20 n n C5' "H5'2" ADP sing 21 n n C4' O4' ADP sing 22 n n C4' C3' ADP sing 23 n n C4' H4' ADP sing 24 n n O4' C1' ADP sing 25 n n C3' O3' ADP sing 26 n n C3' C2' ADP sing 27 n n C3' H3' ADP sing 28 n n O3' HO3' ADP sing 29 n n C2' O2' ADP sing 30 n n C2' C1' ADP sing 31 n n C2' H2' ADP sing 32 n n O2' HO2' ADP sing 33 n n C1' N9 ADP sing 34 n n C1' H1' ADP sing 35 n n N9 C8 ADP sing 36 n y N9 C4 ADP sing 37 n y C8 N7 ADP doub 38 n y C8 H8 ADP sing 39 n n N7 C5 ADP sing 40 n y C5 C6 ADP sing 41 n y C5 C4 ADP doub 42 n y C6 N6 ADP sing 43 n n C6 N1 ADP doub 44 n y N6 HN61 ADP sing 45 n n N6 HN62 ADP sing 46 n n N1 C2 ADP sing 47 n y C2 N3 ADP doub 48 n y C2 H2 ADP sing 49 n n N3 C4 ADP sing 50 n y # _atom_sites.entry_id 8C1D _atom_sites.fract_transf_matrix[1][1] 0.012294 _atom_sites.fract_transf_matrix[1][2] 0.007098 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014196 _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] 0.00583 _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 B 2 T2F A 1 401 4000 T2F 377 . C 3 ADP A 1 402 1 ADP ADP . D 4 MG A 1 403 1 MG MG . E 4 MG A 1 404 2 MG MG . F 5 T5L A 1 405 1 T5L CHA . G 6 SO4 A 1 406 1 SO4 SO4 . H 6 SO4 A 1 407 2 SO4 SO4 . I 6 SO4 A 1 408 3 SO4 SO4 . J 6 SO4 A 1 409 5 SO4 SO4 . K 6 SO4 A 1 410 6 SO4 SO4 . L 6 SO4 A 1 411 7 SO4 SO4 . M 7 DMS A 1 412 1 DMS DMS . N 7 DMS A 1 413 2 DMS DMS . O 8 ACT A 1 414 1 ACT ACT . P 9 HOH A 1 501 4 HOH HOH . P 9 HOH A 2 502 9 HOH HOH . P 9 HOH A 3 503 27 HOH HOH . P 9 HOH A 4 504 99 HOH HOH . P 9 HOH A 5 505 23 HOH HOH . P 9 HOH A 6 506 82 HOH HOH . P 9 HOH A 7 507 72 HOH HOH . P 9 HOH A 8 508 95 HOH HOH . P 9 HOH A 9 509 97 HOH HOH . P 9 HOH A 10 510 3 HOH HOH . P 9 HOH A 11 511 2 HOH HOH . P 9 HOH A 12 512 100 HOH HOH . P 9 HOH A 13 513 98 HOH HOH . P 9 HOH A 14 514 68 HOH HOH . P 9 HOH A 15 515 92 HOH HOH . P 9 HOH A 16 516 48 HOH HOH . P 9 HOH A 17 517 69 HOH HOH . P 9 HOH A 18 518 7 HOH HOH . P 9 HOH A 19 519 62 HOH HOH . P 9 HOH A 20 520 96 HOH HOH . P 9 HOH A 21 521 19 HOH HOH . P 9 HOH A 22 522 1 HOH HOH . P 9 HOH A 23 523 43 HOH HOH . P 9 HOH A 24 524 6 HOH HOH . P 9 HOH A 25 525 81 HOH HOH . P 9 HOH A 26 526 17 HOH HOH . P 9 HOH A 27 527 93 HOH HOH . P 9 HOH A 28 528 70 HOH HOH . P 9 HOH A 29 529 34 HOH HOH . P 9 HOH A 30 530 35 HOH HOH . P 9 HOH A 31 531 28 HOH HOH . P 9 HOH A 32 532 94 HOH HOH . P 9 HOH A 33 533 139 HOH HOH . P 9 HOH A 34 534 124 HOH HOH . P 9 HOH A 35 535 10 HOH HOH . P 9 HOH A 36 536 40 HOH HOH . P 9 HOH A 37 537 20 HOH HOH . P 9 HOH A 38 538 16 HOH HOH . P 9 HOH A 39 539 140 HOH HOH . P 9 HOH A 40 540 8 HOH HOH . P 9 HOH A 41 541 14 HOH HOH . P 9 HOH A 42 542 31 HOH HOH . P 9 HOH A 43 543 5 HOH HOH . P 9 HOH A 44 544 29 HOH HOH . P 9 HOH A 45 545 38 HOH HOH . P 9 HOH A 46 546 141 HOH HOH . P 9 HOH A 47 547 59 HOH HOH . P 9 HOH A 48 548 12 HOH HOH . P 9 HOH A 49 549 138 HOH HOH . P 9 HOH A 50 550 64 HOH HOH . P 9 HOH A 51 551 54 HOH HOH . P 9 HOH A 52 552 63 HOH HOH . P 9 HOH A 53 553 13 HOH HOH . P 9 HOH A 54 554 137 HOH HOH . P 9 HOH A 55 555 36 HOH HOH . P 9 HOH A 56 556 24 HOH HOH . P 9 HOH A 57 557 121 HOH HOH . P 9 HOH A 58 558 101 HOH HOH . P 9 HOH A 59 559 46 HOH HOH . P 9 HOH A 60 560 15 HOH HOH . P 9 HOH A 61 561 26 HOH HOH . P 9 HOH A 62 562 55 HOH HOH . P 9 HOH A 63 563 11 HOH HOH . P 9 HOH A 64 564 105 HOH HOH . P 9 HOH A 65 565 61 HOH HOH . P 9 HOH A 66 566 132 HOH HOH . P 9 HOH A 67 567 142 HOH HOH . P 9 HOH A 68 568 30 HOH HOH . P 9 HOH A 69 569 80 HOH HOH . P 9 HOH A 70 570 44 HOH HOH . P 9 HOH A 71 571 112 HOH HOH . P 9 HOH A 72 572 41 HOH HOH . P 9 HOH A 73 573 84 HOH HOH . P 9 HOH A 74 574 53 HOH HOH . P 9 HOH A 75 575 58 HOH HOH . P 9 HOH A 76 576 37 HOH HOH . P 9 HOH A 77 577 51 HOH HOH . P 9 HOH A 78 578 60 HOH HOH . P 9 HOH A 79 579 66 HOH HOH . P 9 HOH A 80 580 89 HOH HOH . P 9 HOH A 81 581 78 HOH HOH . P 9 HOH A 82 582 77 HOH HOH . P 9 HOH A 83 583 32 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 PB ADP . . . C 3 -10.038 -23.7 4.74 1 53.47 ? PB ADP 402 A 1 HETATM 2 O O1B ADP . . . C 3 -10.79 -24.697 3.813 1 52.14 ? O1B ADP 402 A 1 HETATM 3 O O2B ADP . . . C 3 -9.407 -22.57 3.951 1 57.59 ? O2B ADP 402 A 1 HETATM 4 O O3B ADP . . . C 3 -10.942 -23.216 5.838 1 49.55 ? O3B ADP 402 A 1 HETATM 5 P PA ADP . . . C 3 -8.508 -25.857 6.007 1 51.48 ? PA ADP 402 A 1 HETATM 6 O O1A ADP . . . C 3 -9.555 -26.87 5.607 1 48.19 ? O1A ADP 402 A 1 HETATM 7 O O2A ADP . . . C 3 -8.379 -25.703 7.487 1 52.58 ? O2A ADP 402 A 1 HETATM 8 O O3A ADP . . . C 3 -8.753 -24.431 5.33 1 52.2 ? O3A ADP 402 A 1 HETATM 9 O O5' ADP . . . C 3 -7.122 -26.286 5.297 1 53.23 ? O5' ADP 402 A 1 HETATM 10 C C5' ADP . . . C 3 -6.886 -26.268 3.866 1 52.37 ? C5' ADP 402 A 1 HETATM 11 C C4' ADP . . . C 3 -6.173 -27.539 3.465 1 49.4 ? C4' ADP 402 A 1 HETATM 12 O O4' ADP . . . C 3 -4.882 -27.621 4.11 1 50 ? O4' ADP 402 A 1 HETATM 13 C C3' ADP . . . C 3 -6.875 -28.834 3.85 1 50.58 ? C3' ADP 402 A 1 HETATM 14 O O3' ADP . . . C 3 -7.953 -29.154 2.973 1 51.25 ? O3' ADP 402 A 1 HETATM 15 C C2' ADP . . . C 3 -5.712 -29.827 3.864 1 50.52 ? C2' ADP 402 A 1 HETATM 16 O O2' ADP . . . C 3 -5.372 -30.181 2.529 1 48.37 ? O2' ADP 402 A 1 HETATM 17 C C1' ADP . . . C 3 -4.606 -28.963 4.488 1 51.4 ? C1' ADP 402 A 1 HETATM 18 N N9 ADP . . . C 3 -4.53 -29.04 5.951 1 51.96 ? N9 ADP 402 A 1 HETATM 19 C C8 ADP . . . C 3 -5.213 -28.251 6.841 1 49.03 ? C8 ADP 402 A 1 HETATM 20 N N7 ADP . . . C 3 -4.933 -28.495 8.099 1 51.16 ? N7 ADP 402 A 1 HETATM 21 C C5 ADP . . . C 3 -3.989 -29.507 8.035 1 50.91 ? C5 ADP 402 A 1 HETATM 22 C C6 ADP . . . C 3 -3.286 -30.219 9.038 1 52 ? C6 ADP 402 A 1 HETATM 23 N N6 ADP . . . C 3 -3.453 -30.014 10.347 1 48.17 ? N6 ADP 402 A 1 HETATM 24 N N1 ADP . . . C 3 -2.428 -31.195 8.64 1 46.95 ? N1 ADP 402 A 1 HETATM 25 C C2 ADP . . . C 3 -2.314 -31.452 7.329 1 49.96 ? C2 ADP 402 A 1 HETATM 26 N N3 ADP . . . C 3 -2.932 -30.855 6.299 1 49.9 ? N3 ADP 402 A 1 HETATM 27 C C4 ADP . . . C 3 -3.746 -29.87 6.719 1 50.06 ? C4 ADP 402 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #