data_1VRP # _model_server_result.job_id V9Wm34DlRVz8i9yc3ZyyoQ _model_server_result.datetime_utc '2024-10-19 02:26:18' _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 1vrp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":400}' # _entry.id 1VRP # _exptl.entry_id 1VRP _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 2 _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 1VRP _cell.length_a 70.634 _cell.length_b 87.189 _cell.length_c 127.596 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VRP _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G 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 D O2B ADP . A ADP 400 1_555 C MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc2 D O1B ADP . A ADP 400 1_555 C MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? metalc ? metalc3 D O1A ADP . A ADP 400 1_555 C MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc4 C MG MG . A MG 404 1_555 I O HOH . A HOH 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc5 C MG MG . A MG 404 1_555 I O HOH . A HOH 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc6 C MG MG . A MG 404 1_555 I O HOH . A HOH 462 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc7 C MG MG . A MG 404 1_555 I O HOH . A HOH 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.038 ? metalc ? metalc8 G O1B ADP . B ADP 401 1_555 E MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc9 G O1A ADP . B ADP 401 1_555 E MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc10 E MG MG . B MG 403 1_555 F O2 NO3 . B NO3 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc11 E MG MG . B MG 403 1_555 J O HOH . B HOH 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc12 E MG MG . B MG 403 1_555 J O HOH . B HOH 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc13 E MG MG . B MG 403 1_555 J O HOH . B HOH 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc14 E MG MG . B MG 403 1_555 J O HOH . B HOH 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? # _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 1VRP _atom_sites.fract_transf_matrix[1][1] 0.014157 _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] 0.011469 _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] 0.007837 _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 C 2 MG A 1 404 404 MG MG . D 3 ADP A 1 400 400 ADP ADP . E 2 MG B 1 403 403 MG MG . F 4 NO3 B 1 405 405 NO3 NO3 . G 3 ADP B 1 401 401 ADP ADP . H 5 IOM B 1 402 402 IOM IOM . I 6 HOH A 1 405 1 HOH HOH . I 6 HOH A 2 406 3 HOH HOH . I 6 HOH A 3 407 6 HOH HOH . I 6 HOH A 4 408 7 HOH HOH . I 6 HOH A 5 409 9 HOH HOH . I 6 HOH A 6 410 11 HOH HOH . I 6 HOH A 7 411 12 HOH HOH . I 6 HOH A 8 412 15 HOH HOH . I 6 HOH A 9 413 25 HOH HOH . I 6 HOH A 10 414 29 HOH HOH . I 6 HOH A 11 415 33 HOH HOH . I 6 HOH A 12 416 34 HOH HOH . I 6 HOH A 13 417 37 HOH HOH . I 6 HOH A 14 418 38 HOH HOH . I 6 HOH A 15 419 39 HOH HOH . I 6 HOH A 16 420 42 HOH HOH . I 6 HOH A 17 421 50 HOH HOH . I 6 HOH A 18 422 51 HOH HOH . I 6 HOH A 19 423 52 HOH HOH . I 6 HOH A 20 424 57 HOH HOH . I 6 HOH A 21 425 60 HOH HOH . I 6 HOH A 22 426 61 HOH HOH . I 6 HOH A 23 427 63 HOH HOH . I 6 HOH A 24 428 64 HOH HOH . I 6 HOH A 25 429 65 HOH HOH . I 6 HOH A 26 430 68 HOH HOH . I 6 HOH A 27 431 69 HOH HOH . I 6 HOH A 28 432 78 HOH HOH . I 6 HOH A 29 433 81 HOH HOH . I 6 HOH A 30 434 83 HOH HOH . I 6 HOH A 31 435 89 HOH HOH . I 6 HOH A 32 436 90 HOH HOH . I 6 HOH A 33 437 91 HOH HOH . I 6 HOH A 34 438 95 HOH HOH . I 6 HOH A 35 439 97 HOH HOH . I 6 HOH A 36 440 98 HOH HOH . I 6 HOH A 37 441 99 HOH HOH . I 6 HOH A 38 442 100 HOH HOH . I 6 HOH A 39 443 101 HOH HOH . I 6 HOH A 40 444 102 HOH HOH . I 6 HOH A 41 445 104 HOH HOH . I 6 HOH A 42 446 108 HOH HOH . I 6 HOH A 43 447 109 HOH HOH . I 6 HOH A 44 448 110 HOH HOH . I 6 HOH A 45 449 111 HOH HOH . I 6 HOH A 46 450 113 HOH HOH . I 6 HOH A 47 451 115 HOH HOH . I 6 HOH A 48 452 117 HOH HOH . I 6 HOH A 49 453 119 HOH HOH . I 6 HOH A 50 454 120 HOH HOH . I 6 HOH A 51 455 121 HOH HOH . I 6 HOH A 52 456 124 HOH HOH . I 6 HOH A 53 457 131 HOH HOH . I 6 HOH A 54 458 134 HOH HOH . I 6 HOH A 55 459 140 HOH HOH . I 6 HOH A 56 460 141 HOH HOH . I 6 HOH A 57 461 142 HOH HOH . I 6 HOH A 58 462 143 HOH HOH . I 6 HOH A 59 463 144 HOH HOH . I 6 HOH A 60 464 145 HOH HOH . I 6 HOH A 61 465 147 HOH HOH . I 6 HOH A 62 466 148 HOH HOH . I 6 HOH A 63 467 149 HOH HOH . I 6 HOH A 64 468 150 HOH HOH . I 6 HOH A 65 469 151 HOH HOH . I 6 HOH A 66 470 152 HOH HOH . I 6 HOH A 67 471 153 HOH HOH . I 6 HOH A 68 472 154 HOH HOH . J 6 HOH B 1 406 2 HOH HOH . J 6 HOH B 2 407 4 HOH HOH . J 6 HOH B 3 408 5 HOH HOH . J 6 HOH B 4 409 10 HOH HOH . J 6 HOH B 5 410 13 HOH HOH . J 6 HOH B 6 411 14 HOH HOH . J 6 HOH B 7 412 16 HOH HOH . J 6 HOH B 8 413 18 HOH HOH . J 6 HOH B 9 414 19 HOH HOH . J 6 HOH B 10 415 20 HOH HOH . J 6 HOH B 11 416 21 HOH HOH . J 6 HOH B 12 417 22 HOH HOH . J 6 HOH B 13 418 23 HOH HOH . J 6 HOH B 14 419 24 HOH HOH . J 6 HOH B 15 420 26 HOH HOH . J 6 HOH B 16 421 27 HOH HOH . J 6 HOH B 17 422 28 HOH HOH . J 6 HOH B 18 423 30 HOH HOH . J 6 HOH B 19 424 31 HOH HOH . J 6 HOH B 20 425 32 HOH HOH . J 6 HOH B 21 426 35 HOH HOH . J 6 HOH B 22 427 36 HOH HOH . J 6 HOH B 23 428 40 HOH HOH . J 6 HOH B 24 429 41 HOH HOH . J 6 HOH B 25 430 43 HOH HOH . J 6 HOH B 26 431 44 HOH HOH . J 6 HOH B 27 432 45 HOH HOH . J 6 HOH B 28 433 46 HOH HOH . J 6 HOH B 29 434 47 HOH HOH . J 6 HOH B 30 435 48 HOH HOH . J 6 HOH B 31 436 49 HOH HOH . J 6 HOH B 32 437 53 HOH HOH . J 6 HOH B 33 438 54 HOH HOH . J 6 HOH B 34 439 55 HOH HOH . J 6 HOH B 35 440 56 HOH HOH . J 6 HOH B 36 441 58 HOH HOH . J 6 HOH B 37 442 59 HOH HOH . J 6 HOH B 38 443 62 HOH HOH . J 6 HOH B 39 444 66 HOH HOH . J 6 HOH B 40 445 70 HOH HOH . J 6 HOH B 41 446 71 HOH HOH . J 6 HOH B 42 447 73 HOH HOH . J 6 HOH B 43 448 76 HOH HOH . J 6 HOH B 44 449 77 HOH HOH . J 6 HOH B 45 450 79 HOH HOH . J 6 HOH B 46 451 80 HOH HOH . J 6 HOH B 47 452 82 HOH HOH . J 6 HOH B 48 453 84 HOH HOH . J 6 HOH B 49 454 85 HOH HOH . J 6 HOH B 50 455 86 HOH HOH . J 6 HOH B 51 456 87 HOH HOH . J 6 HOH B 52 457 88 HOH HOH . J 6 HOH B 53 458 92 HOH HOH . J 6 HOH B 54 459 93 HOH HOH . J 6 HOH B 55 460 94 HOH HOH . J 6 HOH B 56 461 96 HOH HOH . J 6 HOH B 57 462 103 HOH HOH . J 6 HOH B 58 463 105 HOH HOH . J 6 HOH B 59 464 106 HOH HOH . J 6 HOH B 60 465 107 HOH HOH . J 6 HOH B 61 466 112 HOH HOH . J 6 HOH B 62 467 114 HOH HOH . J 6 HOH B 63 468 116 HOH HOH . J 6 HOH B 64 469 118 HOH HOH . J 6 HOH B 65 470 122 HOH HOH . J 6 HOH B 66 471 123 HOH HOH . J 6 HOH B 67 472 125 HOH HOH . J 6 HOH B 68 473 126 HOH HOH . J 6 HOH B 69 474 127 HOH HOH . J 6 HOH B 70 475 128 HOH HOH . J 6 HOH B 71 476 129 HOH HOH . J 6 HOH B 72 477 130 HOH HOH . J 6 HOH B 73 478 132 HOH HOH . J 6 HOH B 74 479 133 HOH HOH . J 6 HOH B 75 480 135 HOH HOH . J 6 HOH B 76 481 136 HOH HOH . J 6 HOH B 77 482 137 HOH HOH . J 6 HOH B 78 483 138 HOH HOH . J 6 HOH B 79 484 139 HOH HOH . J 6 HOH B 80 485 146 HOH HOH . J 6 HOH B 81 486 155 HOH HOH . J 6 HOH B 82 487 156 HOH HOH . J 6 HOH B 83 488 157 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 . . . D 3 23.374 32.775 49.63 1 23.55 ? PB ADP 400 A 1 HETATM 2 O O1B ADP . . . D 3 23.706 33.785 48.624 1 22.37 ? O1B ADP 400 A 1 HETATM 3 O O2B ADP . . . D 3 21.924 32.762 49.894 1 24.79 ? O2B ADP 400 A 1 HETATM 4 O O3B ADP . . . D 3 23.872 31.437 49.202 1 24.7 ? O3B ADP 400 A 1 HETATM 5 P PA ADP . . . D 3 24.784 34.437 51.62 1 25.28 ? PA ADP 400 A 1 HETATM 6 O O1A ADP . . . D 3 23.945 35.534 51.066 1 24.83 ? O1A ADP 400 A 1 HETATM 7 O O2A ADP . . . D 3 26.235 34.584 51.362 1 24.2 ? O2A ADP 400 A 1 HETATM 8 O O3A ADP . . . D 3 24.275 33.267 50.976 1 25.69 ? O3A ADP 400 A 1 HETATM 9 O O5' ADP . . . D 3 24.474 33.906 52.978 1 25.59 ? O5' ADP 400 A 1 HETATM 10 C C5' ADP . . . D 3 23.091 33.814 53.351 1 25.7 ? C5' ADP 400 A 1 HETATM 11 C C4' ADP . . . D 3 22.961 33.034 54.659 1 25.83 ? C4' ADP 400 A 1 HETATM 12 O O4' ADP . . . D 3 23.297 31.644 54.454 1 26.27 ? O4' ADP 400 A 1 HETATM 13 C C3' ADP . . . D 3 23.886 33.533 55.76 1 27.65 ? C3' ADP 400 A 1 HETATM 14 O O3' ADP . . . D 3 23.189 33.541 57.015 1 25.71 ? O3' ADP 400 A 1 HETATM 15 C C2' ADP . . . D 3 25.042 32.553 55.752 1 26.36 ? C2' ADP 400 A 1 HETATM 16 O O2' ADP . . . D 3 25.771 32.59 56.975 1 27.63 ? O2' ADP 400 A 1 HETATM 17 C C1' ADP . . . D 3 24.297 31.265 55.432 1 27.32 ? C1' ADP 400 A 1 HETATM 18 N N9 ADP . . . D 3 25.203 30.197 54.899 1 27.51 ? N9 ADP 400 A 1 HETATM 19 C C8 ADP . . . D 3 25.882 30.151 53.734 1 26.78 ? C8 ADP 400 A 1 HETATM 20 N N7 ADP . . . D 3 26.597 29.014 53.634 1 28.56 ? N7 ADP 400 A 1 HETATM 21 C C5 ADP . . . D 3 26.335 28.367 54.763 1 27.67 ? C5 ADP 400 A 1 HETATM 22 C C6 ADP . . . D 3 26.857 27.104 55.148 1 27.32 ? C6 ADP 400 A 1 HETATM 23 N N6 ADP . . . D 3 27.696 26.383 54.399 1 25.54 ? N6 ADP 400 A 1 HETATM 24 N N1 ADP . . . D 3 26.435 26.642 56.362 1 26.92 ? N1 ADP 400 A 1 HETATM 25 C C2 ADP . . . D 3 25.59 27.353 57.131 1 26.55 ? C2 ADP 400 A 1 HETATM 26 N N3 ADP . . . D 3 25.102 28.552 56.763 1 25.83 ? N3 ADP 400 A 1 HETATM 27 C C4 ADP . . . D 3 25.471 29.088 55.569 1 26.89 ? C4 ADP 400 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 383 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #