data_5ORZ # _model_server_result.job_id w7bidAI2rnRdy8JtFeKcWg _model_server_result.datetime_utc '2024-11-23 21:44:41' _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 5orz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5ORZ # _exptl.entry_id 5ORZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 5ORZ _cell.length_a 81.97 _cell.length_b 81.97 _cell.length_c 175.49 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ORZ _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 _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 2 _struct_asym.id B _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 A C THR 161 A THR 287 1_555 A N TPO 162 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C TPO 162 A TPO 288 1_555 A N LEU 163 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD1 ASN 135 A ASN 261 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc2 A OD2 ASP 148 A ASP 274 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc3 A OD1 ASP 148 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc4 B O3B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc5 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc6 B O1B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc7 C MG MG . A MG 402 1_555 I O HOH . A HOH 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc8 C MG MG . A MG 402 1_555 I O HOH . A HOH 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc9 D MG MG . A MG 403 1_555 I O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc10 D MG MG . A MG 403 1_555 I O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc11 D MG MG . A MG 403 1_555 I O HOH . A HOH 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc12 D MG MG . A MG 403 1_555 I O HOH . A HOH 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc13 D MG MG . A MG 403 1_555 I O HOH . A HOH 588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? # _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 26 n n PB O2B ADP sing 27 n n PB O3B ADP sing 28 n n PB O3A ADP sing 29 n n O2B HOB2 ADP sing 30 n n O3B HOB3 ADP sing 31 n n PA O1A ADP doub 32 n n PA O2A ADP sing 33 n n PA O3A ADP sing 34 n n PA O5' ADP sing 35 n n O2A HOA2 ADP sing 36 n n O5' C5' ADP sing 37 n n C5' C4' ADP sing 38 n n C5' "H5'1" ADP sing 39 n n C5' "H5'2" ADP sing 40 n n C4' O4' ADP sing 41 n n C4' C3' ADP sing 42 n n C4' H4' ADP sing 43 n n O4' C1' ADP sing 44 n n C3' O3' ADP sing 45 n n C3' C2' ADP sing 46 n n C3' H3' ADP sing 47 n n O3' HO3' ADP sing 48 n n C2' O2' ADP sing 49 n n C2' C1' ADP sing 50 n n C2' H2' ADP sing 51 n n O2' HO2' ADP sing 52 n n C1' N9 ADP sing 53 n n C1' H1' ADP sing 54 n n N9 C8 ADP sing 55 n y N9 C4 ADP sing 56 n y C8 N7 ADP doub 57 n y C8 H8 ADP sing 58 n n N7 C5 ADP sing 59 n y C5 C6 ADP sing 60 n y C5 C4 ADP doub 61 n y C6 N6 ADP sing 62 n n C6 N1 ADP doub 63 n y N6 HN61 ADP sing 64 n n N6 HN62 ADP sing 65 n n N1 C2 ADP sing 66 n y C2 N3 ADP doub 67 n y C2 H2 ADP sing 68 n n N3 C4 ADP sing 69 n y # _atom_sites.entry_id 5ORZ _atom_sites.fract_transf_matrix[1][1] 0.0122 _atom_sites.fract_transf_matrix[1][2] 0.007043 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014087 _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] 0.005698 _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 ADP A 1 401 1392 ADP ADP . C 3 MG A 1 402 1395 MG MG . D 3 MG A 1 403 1396 MG MG . E 4 CL A 1 404 1397 CL CL . F 4 CL A 1 405 1398 CL CL . G 4 CL A 1 406 1399 CL CL . H 5 A6W A 1 407 1 A6W FRG . I 6 HOH A 1 501 73 HOH HOH . I 6 HOH A 2 502 67 HOH HOH . I 6 HOH A 3 503 46 HOH HOH . I 6 HOH A 4 504 51 HOH HOH . I 6 HOH A 5 505 78 HOH HOH . I 6 HOH A 6 506 6 HOH HOH . I 6 HOH A 7 507 101 HOH HOH . I 6 HOH A 8 508 87 HOH HOH . I 6 HOH A 9 509 18 HOH HOH . I 6 HOH A 10 510 33 HOH HOH . I 6 HOH A 11 511 11 HOH HOH . I 6 HOH A 12 512 72 HOH HOH . I 6 HOH A 13 513 7 HOH HOH . I 6 HOH A 14 514 65 HOH HOH . I 6 HOH A 15 515 55 HOH HOH . I 6 HOH A 16 516 80 HOH HOH . I 6 HOH A 17 517 81 HOH HOH . I 6 HOH A 18 518 58 HOH HOH . I 6 HOH A 19 519 2 HOH HOH . I 6 HOH A 20 520 23 HOH HOH . I 6 HOH A 21 521 10 HOH HOH . I 6 HOH A 22 522 30 HOH HOH . I 6 HOH A 23 523 15 HOH HOH . I 6 HOH A 24 524 12 HOH HOH . I 6 HOH A 25 525 50 HOH HOH . I 6 HOH A 26 526 25 HOH HOH . I 6 HOH A 27 527 14 HOH HOH . I 6 HOH A 28 528 22 HOH HOH . I 6 HOH A 29 529 66 HOH HOH . I 6 HOH A 30 530 31 HOH HOH . I 6 HOH A 31 531 49 HOH HOH . I 6 HOH A 32 532 17 HOH HOH . I 6 HOH A 33 533 47 HOH HOH . I 6 HOH A 34 534 37 HOH HOH . I 6 HOH A 35 535 1 HOH HOH . I 6 HOH A 36 536 34 HOH HOH . I 6 HOH A 37 537 20 HOH HOH . I 6 HOH A 38 538 53 HOH HOH . I 6 HOH A 39 539 21 HOH HOH . I 6 HOH A 40 540 13 HOH HOH . I 6 HOH A 41 541 74 HOH HOH . I 6 HOH A 42 542 8 HOH HOH . I 6 HOH A 43 543 60 HOH HOH . I 6 HOH A 44 544 5 HOH HOH . I 6 HOH A 45 545 36 HOH HOH . I 6 HOH A 46 546 52 HOH HOH . I 6 HOH A 47 547 32 HOH HOH . I 6 HOH A 48 548 38 HOH HOH . I 6 HOH A 49 549 43 HOH HOH . I 6 HOH A 50 550 79 HOH HOH . I 6 HOH A 51 551 9 HOH HOH . I 6 HOH A 52 552 100 HOH HOH . I 6 HOH A 53 553 70 HOH HOH . I 6 HOH A 54 554 63 HOH HOH . I 6 HOH A 55 555 35 HOH HOH . I 6 HOH A 56 556 75 HOH HOH . I 6 HOH A 57 557 26 HOH HOH . I 6 HOH A 58 558 39 HOH HOH . I 6 HOH A 59 559 44 HOH HOH . I 6 HOH A 60 560 77 HOH HOH . I 6 HOH A 61 561 19 HOH HOH . I 6 HOH A 62 562 4 HOH HOH . I 6 HOH A 63 563 56 HOH HOH . I 6 HOH A 64 564 54 HOH HOH . I 6 HOH A 65 565 3 HOH HOH . I 6 HOH A 66 566 69 HOH HOH . I 6 HOH A 67 567 24 HOH HOH . I 6 HOH A 68 568 61 HOH HOH . I 6 HOH A 69 569 95 HOH HOH . I 6 HOH A 70 570 48 HOH HOH . I 6 HOH A 71 571 71 HOH HOH . I 6 HOH A 72 572 62 HOH HOH . I 6 HOH A 73 573 27 HOH HOH . I 6 HOH A 74 574 40 HOH HOH . I 6 HOH A 75 575 59 HOH HOH . I 6 HOH A 76 576 28 HOH HOH . I 6 HOH A 77 577 41 HOH HOH . I 6 HOH A 78 578 76 HOH HOH . I 6 HOH A 79 579 82 HOH HOH . I 6 HOH A 80 580 97 HOH HOH . I 6 HOH A 81 581 99 HOH HOH . I 6 HOH A 82 582 16 HOH HOH . I 6 HOH A 83 583 93 HOH HOH . I 6 HOH A 84 584 104 HOH HOH . I 6 HOH A 85 585 57 HOH HOH . I 6 HOH A 86 586 83 HOH HOH . I 6 HOH A 87 587 96 HOH HOH . I 6 HOH A 88 588 42 HOH HOH . I 6 HOH A 89 589 103 HOH HOH . I 6 HOH A 90 590 45 HOH HOH . I 6 HOH A 91 591 94 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 . . . B 2 -12.063 24.116 -5.833 1 48.78 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -12.706 23.972 -7.19 1 57.18 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -11.596 22.81 -5.236 1 49.82 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -12.808 25.015 -4.875 1 49.65 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -10.626 26.324 -6.887 1 68.3 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -10.415 26.112 -8.365 1 59.9 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -11.772 27.169 -6.388 1 48.93 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -10.686 24.905 -6.127 1 46.86 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -9.273 26.921 -6.25 1 43.91 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -9.054 26.766 -4.851 1 35.35 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -8.244 27.936 -4.312 1 34.89 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -6.985 28.04 -4.981 1 46.32 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -8.953 29.258 -4.545 1 40.96 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -9.802 29.599 -3.446 1 41.05 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -7.811 30.236 -4.7 1 44.56 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -7.434 30.707 -3.405 1 46.22 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -6.673 29.407 -5.264 1 40.84 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -6.62 29.589 -6.737 1 36.65 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -7.327 28.869 -7.628 1 42.44 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -7.072 29.265 -8.9 1 39.87 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -6.177 30.268 -8.835 1 40.23 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -5.481 31.134 -9.814 1 42.61 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -5.701 30.999 -11.146 1 43.44 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -4.622 32.062 -9.333 1 41.52 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -4.4 32.201 -8.012 1 39.94 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -4.996 31.449 -7.069 1 42.18 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -5.882 30.48 -7.408 1 36.15 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #