data_3EQH # _model_server_result.job_id Qna-e-_qDtZPKOz3NDIgRQ _model_server_result.datetime_utc '2024-11-27 03:05:53' _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 3eqh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2}' # _entry.id 3EQH # _exptl.entry_id 3EQH _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 3EQH _cell.length_a 76.61 _cell.length_b 76.61 _cell.length_c 222.9 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EQH _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS monomeric 1 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 11_555 -x+y,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 111.45 # _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 C O1B ADP . A ADP 2 1_555 D MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc2 C O2A ADP . A ADP 2 1_555 D MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc3 D MG MG . A MG 3 1_555 A OD1 ASN 162 A ASN 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc4 D MG MG . A MG 3 1_555 A OD2 ASP 175 A ASP 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc5 D MG MG . A MG 3 1_555 G O HOH . A HOH 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc6 D MG MG . A MG 3 1_555 G O HOH . A HOH 532 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc7 E CA CA . A CA 5 1_555 A OD1 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 4.583 ? metalc ? metalc8 E CA CA . A CA 5 1_555 A OD2 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc9 E CA CA . A CA 5 1_555 A OD1 ASP 33 A ASP 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc10 E CA CA . A CA 5 1_555 G O HOH . A HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc11 F NA NA . A NA 6 1_555 A OD1 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc12 F NA NA . A NA 6 1_555 A OD2 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc13 F NA NA . A NA 6 1_555 G O HOH . A HOH 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? metalc ? metalc14 F NA NA . A NA 6 1_555 G O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? # _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 44 n n PB O2B ADP sing 45 n n PB O3B ADP sing 46 n n PB O3A ADP sing 47 n n O2B HOB2 ADP sing 48 n n O3B HOB3 ADP sing 49 n n PA O1A ADP doub 50 n n PA O2A ADP sing 51 n n PA O3A ADP sing 52 n n PA O5' ADP sing 53 n n O2A HOA2 ADP sing 54 n n O5' C5' ADP sing 55 n n C5' C4' ADP sing 56 n n C5' "H5'1" ADP sing 57 n n C5' "H5'2" ADP sing 58 n n C4' O4' ADP sing 59 n n C4' C3' ADP sing 60 n n C4' H4' ADP sing 61 n n O4' C1' ADP sing 62 n n C3' O3' ADP sing 63 n n C3' C2' ADP sing 64 n n C3' H3' ADP sing 65 n n O3' HO3' ADP sing 66 n n C2' O2' ADP sing 67 n n C2' C1' ADP sing 68 n n C2' H2' ADP sing 69 n n O2' HO2' ADP sing 70 n n C1' N9 ADP sing 71 n n C1' H1' ADP sing 72 n n N9 C8 ADP sing 73 n y N9 C4 ADP sing 74 n y C8 N7 ADP doub 75 n y C8 H8 ADP sing 76 n n N7 C5 ADP sing 77 n y C5 C6 ADP sing 78 n y C5 C4 ADP doub 79 n y C6 N6 ADP sing 80 n n C6 N1 ADP doub 81 n y N6 HN61 ADP sing 82 n n N6 HN62 ADP sing 83 n n N1 C2 ADP sing 84 n y C2 N3 ADP doub 85 n y C2 H2 ADP sing 86 n n N3 C4 ADP sing 87 n y # _atom_sites.entry_id 3EQH _atom_sites.fract_transf_matrix[1][1] 0.013053 _atom_sites.fract_transf_matrix[1][2] 0.007536 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015072 _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] 0.004486 _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 5BM A 1 1 1 5BM 5BM . C 3 ADP A 1 2 2 ADP ADP . D 4 MG A 1 3 3 MG MG . E 5 CA A 1 5 5 CA CA . F 6 NA A 1 6 6 NA NA . G 7 HOH A 1 394 394 HOH HOH . G 7 HOH A 2 395 395 HOH HOH . G 7 HOH A 3 396 396 HOH HOH . G 7 HOH A 4 397 397 HOH HOH . G 7 HOH A 5 398 398 HOH HOH . G 7 HOH A 6 399 399 HOH HOH . G 7 HOH A 7 400 400 HOH HOH . G 7 HOH A 8 401 401 HOH HOH . G 7 HOH A 9 402 402 HOH HOH . G 7 HOH A 10 403 403 HOH HOH . G 7 HOH A 11 404 404 HOH HOH . G 7 HOH A 12 405 405 HOH HOH . G 7 HOH A 13 406 406 HOH HOH . G 7 HOH A 14 407 407 HOH HOH . G 7 HOH A 15 408 408 HOH HOH . G 7 HOH A 16 409 409 HOH HOH . G 7 HOH A 17 410 410 HOH HOH . G 7 HOH A 18 411 411 HOH HOH . G 7 HOH A 19 412 412 HOH HOH . G 7 HOH A 20 413 413 HOH HOH . G 7 HOH A 21 414 414 HOH HOH . G 7 HOH A 22 415 415 HOH HOH . G 7 HOH A 23 416 416 HOH HOH . G 7 HOH A 24 417 417 HOH HOH . G 7 HOH A 25 418 418 HOH HOH . G 7 HOH A 26 419 419 HOH HOH . G 7 HOH A 27 420 420 HOH HOH . G 7 HOH A 28 421 421 HOH HOH . G 7 HOH A 29 422 422 HOH HOH . G 7 HOH A 30 423 423 HOH HOH . G 7 HOH A 31 424 424 HOH HOH . G 7 HOH A 32 425 425 HOH HOH . G 7 HOH A 33 426 426 HOH HOH . G 7 HOH A 34 427 427 HOH HOH . G 7 HOH A 35 428 428 HOH HOH . G 7 HOH A 36 429 429 HOH HOH . G 7 HOH A 37 430 430 HOH HOH . G 7 HOH A 38 431 431 HOH HOH . G 7 HOH A 39 432 432 HOH HOH . G 7 HOH A 40 433 433 HOH HOH . G 7 HOH A 41 434 434 HOH HOH . G 7 HOH A 42 435 435 HOH HOH . G 7 HOH A 43 436 436 HOH HOH . G 7 HOH A 44 437 437 HOH HOH . G 7 HOH A 45 438 438 HOH HOH . G 7 HOH A 46 439 439 HOH HOH . G 7 HOH A 47 440 440 HOH HOH . G 7 HOH A 48 441 441 HOH HOH . G 7 HOH A 49 442 442 HOH HOH . G 7 HOH A 50 443 443 HOH HOH . G 7 HOH A 51 444 444 HOH HOH . G 7 HOH A 52 445 445 HOH HOH . G 7 HOH A 53 446 446 HOH HOH . G 7 HOH A 54 447 447 HOH HOH . G 7 HOH A 55 448 448 HOH HOH . G 7 HOH A 56 449 449 HOH HOH . G 7 HOH A 57 450 450 HOH HOH . G 7 HOH A 58 451 451 HOH HOH . G 7 HOH A 59 452 452 HOH HOH . G 7 HOH A 60 453 453 HOH HOH . G 7 HOH A 61 454 454 HOH HOH . G 7 HOH A 62 455 455 HOH HOH . G 7 HOH A 63 456 456 HOH HOH . G 7 HOH A 64 457 457 HOH HOH . G 7 HOH A 65 458 458 HOH HOH . G 7 HOH A 66 459 459 HOH HOH . G 7 HOH A 67 460 460 HOH HOH . G 7 HOH A 68 461 461 HOH HOH . G 7 HOH A 69 462 462 HOH HOH . G 7 HOH A 70 463 463 HOH HOH . G 7 HOH A 71 464 464 HOH HOH . G 7 HOH A 72 465 465 HOH HOH . G 7 HOH A 73 466 466 HOH HOH . G 7 HOH A 74 467 467 HOH HOH . G 7 HOH A 75 468 468 HOH HOH . G 7 HOH A 76 469 469 HOH HOH . G 7 HOH A 77 470 470 HOH HOH . G 7 HOH A 78 471 471 HOH HOH . G 7 HOH A 79 472 472 HOH HOH . G 7 HOH A 80 473 473 HOH HOH . G 7 HOH A 81 474 474 HOH HOH . G 7 HOH A 82 475 475 HOH HOH . G 7 HOH A 83 476 476 HOH HOH . G 7 HOH A 84 477 477 HOH HOH . G 7 HOH A 85 478 478 HOH HOH . G 7 HOH A 86 479 479 HOH HOH . G 7 HOH A 87 480 480 HOH HOH . G 7 HOH A 88 481 481 HOH HOH . G 7 HOH A 89 482 482 HOH HOH . G 7 HOH A 90 483 483 HOH HOH . G 7 HOH A 91 484 484 HOH HOH . G 7 HOH A 92 485 485 HOH HOH . G 7 HOH A 93 486 486 HOH HOH . G 7 HOH A 94 487 487 HOH HOH . G 7 HOH A 95 488 488 HOH HOH . G 7 HOH A 96 489 489 HOH HOH . G 7 HOH A 97 490 490 HOH HOH . G 7 HOH A 98 491 491 HOH HOH . G 7 HOH A 99 492 492 HOH HOH . G 7 HOH A 100 493 493 HOH HOH . G 7 HOH A 101 494 494 HOH HOH . G 7 HOH A 102 495 495 HOH HOH . G 7 HOH A 103 496 496 HOH HOH . G 7 HOH A 104 497 497 HOH HOH . G 7 HOH A 105 498 498 HOH HOH . G 7 HOH A 106 499 499 HOH HOH . G 7 HOH A 107 500 500 HOH HOH . G 7 HOH A 108 501 501 HOH HOH . G 7 HOH A 109 502 502 HOH HOH . G 7 HOH A 110 503 503 HOH HOH . G 7 HOH A 111 504 504 HOH HOH . G 7 HOH A 112 505 505 HOH HOH . G 7 HOH A 113 506 506 HOH HOH . G 7 HOH A 114 507 507 HOH HOH . G 7 HOH A 115 508 508 HOH HOH . G 7 HOH A 116 509 509 HOH HOH . G 7 HOH A 117 510 510 HOH HOH . G 7 HOH A 118 511 511 HOH HOH . G 7 HOH A 119 512 512 HOH HOH . G 7 HOH A 120 513 513 HOH HOH . G 7 HOH A 121 514 514 HOH HOH . G 7 HOH A 122 515 515 HOH HOH . G 7 HOH A 123 516 516 HOH HOH . G 7 HOH A 124 517 517 HOH HOH . G 7 HOH A 125 518 518 HOH HOH . G 7 HOH A 126 519 519 HOH HOH . G 7 HOH A 127 520 520 HOH HOH . G 7 HOH A 128 521 521 HOH HOH . G 7 HOH A 129 522 522 HOH HOH . G 7 HOH A 130 523 523 HOH HOH . G 7 HOH A 131 524 524 HOH HOH . G 7 HOH A 132 525 525 HOH HOH . G 7 HOH A 133 526 526 HOH HOH . G 7 HOH A 134 527 527 HOH HOH . G 7 HOH A 135 528 528 HOH HOH . G 7 HOH A 136 529 529 HOH HOH . G 7 HOH A 137 530 530 HOH HOH . G 7 HOH A 138 531 531 HOH HOH . G 7 HOH A 139 532 532 HOH HOH . G 7 HOH A 140 533 533 HOH HOH . G 7 HOH A 141 534 534 HOH HOH . G 7 HOH A 142 535 535 HOH HOH . G 7 HOH A 143 536 393 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 -10.146 62.939 32.961 1 50.25 ? PB ADP 2 A 1 HETATM 2 O O1B ADP . . . C 3 -8.808 63.224 32.359 1 50.72 ? O1B ADP 2 A 1 HETATM 3 O O2B ADP . . . C 3 -11.182 64.069 32.531 1 52.08 ? O2B ADP 2 A 1 HETATM 4 O O3B ADP . . . C 3 -10.671 61.53 32.438 1 51 ? O3B ADP 2 A 1 HETATM 5 P PA ADP . . . C 3 -8.564 63.173 35.126 1 51.07 ? PA ADP 2 A 1 HETATM 6 O O1A ADP . . . C 3 -8.496 62.765 36.563 1 50.85 ? O1A ADP 2 A 1 HETATM 7 O O2A ADP . . . C 3 -7.508 62.315 34.289 1 52.31 ? O2A ADP 2 A 1 HETATM 8 O O3A ADP . . . C 3 -10.059 62.907 34.579 1 51.05 ? O3A ADP 2 A 1 HETATM 9 O O5' ADP . . . C 3 -8.192 64.735 35.007 1 52.45 ? O5' ADP 2 A 1 HETATM 10 C C5' ADP . . . C 3 -9.273 65.507 35.522 1 50.51 ? C5' ADP 2 A 1 HETATM 11 C C4' ADP . . . C 3 -9.178 66.915 34.941 1 50.09 ? C4' ADP 2 A 1 HETATM 12 O O4' ADP . . . C 3 -8.078 67.633 35.556 1 50.27 ? O4' ADP 2 A 1 HETATM 13 C C3' ADP . . . C 3 -8.822 66.843 33.454 1 50.82 ? C3' ADP 2 A 1 HETATM 14 O O3' ADP . . . C 3 -10.002 66.689 32.66 1 52.44 ? O3' ADP 2 A 1 HETATM 15 C C2' ADP . . . C 3 -8.152 68.198 33.2 1 50.77 ? C2' ADP 2 A 1 HETATM 16 O O2' ADP . . . C 3 -9.137 69.166 32.84 1 52.99 ? O2' ADP 2 A 1 HETATM 17 C C1' ADP . . . C 3 -7.515 68.55 34.564 1 50.11 ? C1' ADP 2 A 1 HETATM 18 N N9 ADP . . . C 3 -6.052 68.408 34.526 1 49.05 ? N9 ADP 2 A 1 HETATM 19 C C8 ADP . . . C 3 -5.351 67.234 34.561 1 49.13 ? C8 ADP 2 A 1 HETATM 20 N N7 ADP . . . C 3 -4.067 67.471 34.517 1 47.67 ? N7 ADP 2 A 1 HETATM 21 C C5 ADP . . . C 3 -3.87 68.82 34.457 1 47.55 ? C5 ADP 2 A 1 HETATM 22 C C6 ADP . . . C 3 -2.726 69.649 34.398 1 47.5 ? C6 ADP 2 A 1 HETATM 23 N N6 ADP . . . C 3 -1.449 69.109 34.388 1 47.38 ? N6 ADP 2 A 1 HETATM 24 N N1 ADP . . . C 3 -2.901 70.971 34.353 1 47.69 ? N1 ADP 2 A 1 HETATM 25 C C2 ADP . . . C 3 -4.122 71.496 34.351 1 48.48 ? C2 ADP 2 A 1 HETATM 26 N N3 ADP . . . C 3 -5.231 70.765 34.406 1 48.21 ? N3 ADP 2 A 1 HETATM 27 C C4 ADP . . . C 3 -5.134 69.433 34.462 1 47.88 ? C4 ADP 2 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #