data_1JBP # _model_server_result.job_id HWJHe8xhfojGhpDOBFRbNw _model_server_result.datetime_utc '2024-10-13 08:15:25' _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 1jbp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":381}' # _entry.id 1JBP # _exptl.entry_id 1JBP _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 90 _cell.entry_id 1JBP _cell.length_a 73.96 _cell.length_b 76.11 _cell.length_c 81 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JBP _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 covale ? covale1 A C GLY 9 E GLY 9 1_555 A N SEP 10 E SEP 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C SEP 10 E SEP 10 1_555 A N GLU 11 E GLU 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale3 A C TRP 196 E TRP 196 1_555 A N TPO 197 E TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C TPO 197 E TPO 197 1_555 A N LEU 198 E LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale5 A C VAL 337 E VAL 337 1_555 A N SEP 338 E SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale6 A C SEP 338 E SEP 338 1_555 A N ILE 339 E ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? # _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 1JBP _atom_sites.fract_transf_matrix[1][1] 0.013521 _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] 0.013139 _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] 0.012346 _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 3 ADP E 1 381 381 ADP ADP . D 4 OCT E 1 382 382 OCT OCT . E 5 HOH E 1 383 383 HOH WAT . E 5 HOH E 2 384 384 HOH WAT . E 5 HOH E 3 385 385 HOH WAT . E 5 HOH E 4 386 386 HOH WAT . E 5 HOH E 5 387 387 HOH WAT . E 5 HOH E 6 388 388 HOH WAT . E 5 HOH E 7 389 389 HOH WAT . E 5 HOH E 8 390 390 HOH WAT . E 5 HOH E 9 393 393 HOH WAT . E 5 HOH E 10 395 395 HOH WAT . E 5 HOH E 11 396 396 HOH WAT . E 5 HOH E 12 397 397 HOH WAT . E 5 HOH E 13 398 398 HOH WAT . E 5 HOH E 14 399 399 HOH WAT . E 5 HOH E 15 400 400 HOH WAT . E 5 HOH E 16 401 401 HOH WAT . E 5 HOH E 17 402 402 HOH WAT . E 5 HOH E 18 404 404 HOH WAT . E 5 HOH E 19 405 405 HOH WAT . E 5 HOH E 20 406 406 HOH WAT . E 5 HOH E 21 407 407 HOH WAT . E 5 HOH E 22 408 408 HOH WAT . E 5 HOH E 23 409 409 HOH WAT . E 5 HOH E 24 410 410 HOH WAT . E 5 HOH E 25 411 411 HOH WAT . E 5 HOH E 26 413 413 HOH WAT . E 5 HOH E 27 414 414 HOH WAT . E 5 HOH E 28 415 415 HOH WAT . E 5 HOH E 29 416 416 HOH WAT . E 5 HOH E 30 417 417 HOH WAT . E 5 HOH E 31 419 419 HOH WAT . E 5 HOH E 32 420 420 HOH WAT . E 5 HOH E 33 421 421 HOH WAT . E 5 HOH E 34 422 422 HOH WAT . E 5 HOH E 35 423 423 HOH WAT . E 5 HOH E 36 425 425 HOH WAT . E 5 HOH E 37 426 426 HOH WAT . E 5 HOH E 38 427 427 HOH WAT . E 5 HOH E 39 428 428 HOH WAT . E 5 HOH E 40 429 429 HOH WAT . E 5 HOH E 41 430 430 HOH WAT . E 5 HOH E 42 431 431 HOH WAT . E 5 HOH E 43 434 434 HOH WAT . E 5 HOH E 44 435 435 HOH WAT . E 5 HOH E 45 437 437 HOH WAT . E 5 HOH E 46 438 438 HOH WAT . E 5 HOH E 47 440 440 HOH WAT . E 5 HOH E 48 441 441 HOH WAT . E 5 HOH E 49 443 443 HOH WAT . E 5 HOH E 50 445 445 HOH WAT . E 5 HOH E 51 446 446 HOH WAT . E 5 HOH E 52 447 447 HOH WAT . E 5 HOH E 53 448 448 HOH WAT . E 5 HOH E 54 449 449 HOH WAT . E 5 HOH E 55 450 450 HOH WAT . E 5 HOH E 56 451 451 HOH WAT . E 5 HOH E 57 452 452 HOH WAT . E 5 HOH E 58 453 453 HOH WAT . E 5 HOH E 59 454 454 HOH WAT . E 5 HOH E 60 455 455 HOH WAT . E 5 HOH E 61 456 456 HOH WAT . E 5 HOH E 62 457 457 HOH WAT . E 5 HOH E 63 458 458 HOH WAT . E 5 HOH E 64 459 459 HOH WAT . E 5 HOH E 65 460 460 HOH WAT . E 5 HOH E 66 461 461 HOH WAT . E 5 HOH E 67 462 462 HOH WAT . E 5 HOH E 68 463 463 HOH WAT . E 5 HOH E 69 464 464 HOH WAT . E 5 HOH E 70 465 465 HOH WAT . E 5 HOH E 71 466 466 HOH WAT . E 5 HOH E 72 467 467 HOH WAT . E 5 HOH E 73 468 468 HOH WAT . E 5 HOH E 74 469 469 HOH WAT . E 5 HOH E 75 471 471 HOH WAT . E 5 HOH E 76 472 472 HOH WAT . E 5 HOH E 77 473 473 HOH WAT . E 5 HOH E 78 474 474 HOH WAT . E 5 HOH E 79 475 475 HOH WAT . E 5 HOH E 80 476 476 HOH WAT . E 5 HOH E 81 477 477 HOH WAT . E 5 HOH E 82 478 478 HOH WAT . E 5 HOH E 83 479 479 HOH WAT . E 5 HOH E 84 480 480 HOH WAT . E 5 HOH E 85 481 481 HOH WAT . E 5 HOH E 86 482 482 HOH WAT . E 5 HOH E 87 483 483 HOH WAT . E 5 HOH E 88 484 484 HOH WAT . E 5 HOH E 89 485 485 HOH WAT . E 5 HOH E 90 486 486 HOH WAT . E 5 HOH E 91 487 487 HOH WAT . E 5 HOH E 92 488 488 HOH WAT . E 5 HOH E 93 489 489 HOH WAT . E 5 HOH E 94 490 490 HOH WAT . E 5 HOH E 95 491 491 HOH WAT . E 5 HOH E 96 492 492 HOH WAT . E 5 HOH E 97 493 493 HOH WAT . E 5 HOH E 98 494 494 HOH WAT . E 5 HOH E 99 495 495 HOH WAT . E 5 HOH E 100 496 496 HOH WAT . E 5 HOH E 101 497 497 HOH WAT . E 5 HOH E 102 499 499 HOH WAT . E 5 HOH E 103 501 501 HOH WAT . E 5 HOH E 104 502 502 HOH WAT . E 5 HOH E 105 503 503 HOH WAT . E 5 HOH E 106 504 504 HOH WAT . E 5 HOH E 107 505 505 HOH WAT . E 5 HOH E 108 506 506 HOH WAT . E 5 HOH E 109 507 507 HOH WAT . E 5 HOH E 110 508 508 HOH WAT . E 5 HOH E 111 509 509 HOH WAT . E 5 HOH E 112 510 510 HOH WAT . E 5 HOH E 113 511 511 HOH WAT . E 5 HOH E 114 512 512 HOH WAT . E 5 HOH E 115 513 513 HOH WAT . E 5 HOH E 116 514 514 HOH WAT . E 5 HOH E 117 515 515 HOH WAT . E 5 HOH E 118 516 516 HOH WAT . E 5 HOH E 119 517 517 HOH WAT . E 5 HOH E 120 518 518 HOH WAT . E 5 HOH E 121 520 520 HOH WAT . E 5 HOH E 122 521 521 HOH WAT . E 5 HOH E 123 522 522 HOH WAT . E 5 HOH E 124 523 523 HOH WAT . E 5 HOH E 125 524 524 HOH WAT . E 5 HOH E 126 525 525 HOH WAT . E 5 HOH E 127 526 526 HOH WAT . E 5 HOH E 128 527 527 HOH WAT . E 5 HOH E 129 528 528 HOH WAT . E 5 HOH E 130 529 529 HOH WAT . E 5 HOH E 131 530 530 HOH WAT . E 5 HOH E 132 531 531 HOH WAT . E 5 HOH E 133 532 532 HOH WAT . E 5 HOH E 134 533 533 HOH WAT . E 5 HOH E 135 534 534 HOH WAT . E 5 HOH E 136 535 535 HOH WAT . E 5 HOH E 137 536 536 HOH WAT . E 5 HOH E 138 537 537 HOH WAT . E 5 HOH E 139 538 538 HOH WAT . E 5 HOH E 140 539 539 HOH WAT . E 5 HOH E 141 540 540 HOH WAT . E 5 HOH E 142 541 541 HOH WAT . E 5 HOH E 143 542 542 HOH WAT . E 5 HOH E 144 543 543 HOH WAT . E 5 HOH E 145 544 544 HOH WAT . E 5 HOH E 146 545 545 HOH WAT . E 5 HOH E 147 546 546 HOH WAT . E 5 HOH E 148 549 549 HOH WAT . E 5 HOH E 149 550 550 HOH WAT . F 5 HOH S 1 391 391 HOH WAT . F 5 HOH S 2 392 392 HOH WAT . F 5 HOH S 3 394 394 HOH WAT . F 5 HOH S 4 403 403 HOH WAT . F 5 HOH S 5 412 412 HOH WAT . F 5 HOH S 6 418 418 HOH WAT . F 5 HOH S 7 424 424 HOH WAT . F 5 HOH S 8 432 432 HOH WAT . F 5 HOH S 9 433 433 HOH WAT . F 5 HOH S 10 436 436 HOH WAT . F 5 HOH S 11 439 439 HOH WAT . F 5 HOH S 12 442 442 HOH WAT . F 5 HOH S 13 444 444 HOH WAT . F 5 HOH S 14 470 470 HOH WAT . F 5 HOH S 15 498 498 HOH WAT . F 5 HOH S 16 500 500 HOH WAT . F 5 HOH S 17 519 519 HOH WAT . F 5 HOH S 18 547 547 HOH WAT . F 5 HOH S 19 548 548 HOH WAT . # 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 13.486 11.176 -0.501 1 99.99 ? PB ADP 381 E 1 HETATM 2 O O1B ADP . . . C 3 13.788 12.102 -1.654 1 59.01 ? O1B ADP 381 E 1 HETATM 3 O O2B ADP . . . C 3 14.387 9.989 -0.306 1 73.76 ? O2B ADP 381 E 1 HETATM 4 O O3B ADP . . . C 3 13.306 12.078 0.845 1 99.99 ? O3B ADP 381 E 1 HETATM 5 P PA ADP . . . C 3 11.149 9.545 0.246 1 36.49 ? PA ADP 381 E 1 HETATM 6 O O1A ADP . . . C 3 9.889 9.279 -0.497 1 53.06 ? O1A ADP 381 E 1 HETATM 7 O O2A ADP . . . C 3 12.01 8.36 0.477 1 76.09 ? O2A ADP 381 E 1 HETATM 8 O O3A ADP . . . C 3 11.985 10.633 -0.572 1 91.21 ? O3A ADP 381 E 1 HETATM 9 O O5' ADP . . . C 3 10.803 10.199 1.676 1 32.23 ? O5' ADP 381 E 1 HETATM 10 C C5' ADP . . . C 3 11.544 9.942 2.893 1 15.42 ? C5' ADP 381 E 1 HETATM 11 C C4' ADP . . . C 3 10.623 9.513 4.023 1 16.02 ? C4' ADP 381 E 1 HETATM 12 O O4' ADP . . . C 3 9.405 10.317 4.02 1 6.86 ? O4' ADP 381 E 1 HETATM 13 C C3' ADP . . . C 3 10.086 8.096 3.96 1 14.59 ? C3' ADP 381 E 1 HETATM 14 O O3' ADP . . . C 3 11.085 7.172 4.47 1 18.98 ? O3' ADP 381 E 1 HETATM 15 C C2' ADP . . . C 3 8.97 8.211 4.973 1 15.76 ? C2' ADP 381 E 1 HETATM 16 O O2' ADP . . . C 3 9.538 8.288 6.267 1 10.59 ? O2' ADP 381 E 1 HETATM 17 C C1' ADP . . . C 3 8.35 9.572 4.604 1 18.34 ? C1' ADP 381 E 1 HETATM 18 N N9 ADP . . . C 3 7.204 9.487 3.693 1 17.3 ? N9 ADP 381 E 1 HETATM 19 C C8 ADP . . . C 3 7.23 9.337 2.34 1 14.58 ? C8 ADP 381 E 1 HETATM 20 N N7 ADP . . . C 3 6.063 9.239 1.777 1 29.68 ? N7 ADP 381 E 1 HETATM 21 C C5 ADP . . . C 3 5.186 9.337 2.829 1 16.39 ? C5 ADP 381 E 1 HETATM 22 C C6 ADP . . . C 3 3.777 9.302 2.865 1 31.38 ? C6 ADP 381 E 1 HETATM 23 N N6 ADP . . . C 3 3.008 9.169 1.751 1 12.53 ? N6 ADP 381 E 1 HETATM 24 N N1 ADP . . . C 3 3.213 9.396 4.097 1 26.32 ? N1 ADP 381 E 1 HETATM 25 C C2 ADP . . . C 3 4.014 9.514 5.191 1 3.34 ? C2 ADP 381 E 1 HETATM 26 N N3 ADP . . . C 3 5.36 9.538 5.249 1 11.11 ? N3 ADP 381 E 1 HETATM 27 C C4 ADP . . . C 3 5.878 9.464 4.027 1 48.31 ? C4 ADP 381 E 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #