data_2NVK # _model_server_result.job_id 1y6M2j4gQrl4sxCWn2d8ow _model_server_result.datetime_utc '2025-02-28 06:49:25' _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 2nvk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":490}' # _entry.id 2NVK # _exptl.entry_id 2NVK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 2NVK _cell.length_a 151.487 _cell.length_b 151.487 _cell.length_c 134.259 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NVK _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 17_555 x-y+1/3,-y+2/3,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 87.46106 89.506 # _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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 57 _struct_conn.ptnr1_auth_asym_id X _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 57 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 62 _struct_conn.ptnr2_auth_asym_id X _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 62 _struct_conn.ptnr2_symmetry 1_555 _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 2.055 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C21 H28 N7 O17 P3' _chem_comp.formula_weight 743.405 _chem_comp.id NAP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" # 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 PA O1A NAP doub 328 n n PA O2A NAP sing 329 n n PA O5B NAP sing 330 n n PA O3 NAP sing 331 n n O2A HOA2 NAP sing 332 n n O5B C5B NAP sing 333 n n C5B C4B NAP sing 334 n n C5B H51A NAP sing 335 n n C5B H52A NAP sing 336 n n C4B O4B NAP sing 337 n n C4B C3B NAP sing 338 n n C4B H4B NAP sing 339 n n O4B C1B NAP sing 340 n n C3B O3B NAP sing 341 n n C3B C2B NAP sing 342 n n C3B H3B NAP sing 343 n n O3B HO3A NAP sing 344 n n C2B O2B NAP sing 345 n n C2B C1B NAP sing 346 n n C2B H2B NAP sing 347 n n O2B P2B NAP sing 348 n n C1B N9A NAP sing 349 n n C1B H1B NAP sing 350 n n N9A C8A NAP sing 351 n y N9A C4A NAP sing 352 n y C8A N7A NAP doub 353 n y C8A H8A NAP sing 354 n n N7A C5A NAP sing 355 n y C5A C6A NAP sing 356 n y C5A C4A NAP doub 357 n y C6A N6A NAP sing 358 n n C6A N1A NAP doub 359 n y N6A H61A NAP sing 360 n n N6A H62A NAP sing 361 n n N1A C2A NAP sing 362 n y C2A N3A NAP doub 363 n y C2A H2A NAP sing 364 n n N3A C4A NAP sing 365 n y O3 PN NAP sing 366 n n PN O1N NAP doub 367 n n PN O2N NAP sing 368 n n PN O5D NAP sing 369 n n O5D C5D NAP sing 370 n n C5D C4D NAP sing 371 n n C5D H51N NAP sing 372 n n C5D H52N NAP sing 373 n n C4D O4D NAP sing 374 n n C4D C3D NAP sing 375 n n C4D H4D NAP sing 376 n n O4D C1D NAP sing 377 n n C3D O3D NAP sing 378 n n C3D C2D NAP sing 379 n n C3D H3D NAP sing 380 n n O3D HO3N NAP sing 381 n n C2D O2D NAP sing 382 n n C2D C1D NAP sing 383 n n C2D H2D NAP sing 384 n n O2D HO2N NAP sing 385 n n C1D N1N NAP sing 386 n n C1D H1D NAP sing 387 n n N1N C2N NAP sing 388 n y N1N C6N NAP doub 389 n y C2N C3N NAP doub 390 n y C2N H2N NAP sing 391 n n C3N C7N NAP sing 392 n n C3N C4N NAP sing 393 n y C7N O7N NAP doub 394 n n C7N N7N NAP sing 395 n n N7N H71N NAP sing 396 n n N7N H72N NAP sing 397 n n C4N C5N NAP doub 398 n y C4N H4N NAP sing 399 n n C5N C6N NAP sing 400 n y C5N H5N NAP sing 401 n n C6N H6N NAP sing 402 n n P2B O1X NAP doub 403 n n P2B O2X NAP sing 404 n n P2B O3X NAP sing 405 n n O2X HOP2 NAP sing 406 n n O3X HOP3 NAP sing 407 n n # _atom_sites.entry_id 2NVK _atom_sites.fract_transf_matrix[1][1] 0.006601 _atom_sites.fract_transf_matrix[1][2] 0.003811 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007622 _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] 0.007448 _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 FAD X 1 489 489 FAD FAD . C 3 NAP X 1 490 490 NAP NAP . D 4 HOH X 1 491 491 HOH HOH . D 4 HOH X 2 492 492 HOH HOH . D 4 HOH X 3 493 493 HOH HOH . D 4 HOH X 4 494 494 HOH HOH . D 4 HOH X 5 495 495 HOH HOH . D 4 HOH X 6 496 496 HOH HOH . D 4 HOH X 7 497 497 HOH HOH . D 4 HOH X 8 498 498 HOH HOH . D 4 HOH X 9 499 499 HOH HOH . D 4 HOH X 10 500 500 HOH HOH . D 4 HOH X 11 501 501 HOH HOH . D 4 HOH X 12 502 502 HOH HOH . D 4 HOH X 13 503 503 HOH HOH . D 4 HOH X 14 504 504 HOH HOH . D 4 HOH X 15 505 505 HOH HOH . D 4 HOH X 16 506 506 HOH HOH . D 4 HOH X 17 507 507 HOH HOH . D 4 HOH X 18 508 508 HOH HOH . D 4 HOH X 19 509 509 HOH HOH . D 4 HOH X 20 510 510 HOH HOH . D 4 HOH X 21 511 511 HOH HOH . D 4 HOH X 22 512 512 HOH HOH . D 4 HOH X 23 513 513 HOH HOH . D 4 HOH X 24 514 514 HOH HOH . D 4 HOH X 25 515 515 HOH HOH . D 4 HOH X 26 516 516 HOH HOH . D 4 HOH X 27 517 517 HOH HOH . D 4 HOH X 28 518 518 HOH HOH . D 4 HOH X 29 519 519 HOH HOH . D 4 HOH X 30 520 520 HOH HOH . D 4 HOH X 31 521 521 HOH HOH . D 4 HOH X 32 522 522 HOH HOH . D 4 HOH X 33 523 523 HOH HOH . D 4 HOH X 34 524 524 HOH HOH . D 4 HOH X 35 525 525 HOH HOH . D 4 HOH X 36 526 526 HOH HOH . D 4 HOH X 37 527 527 HOH HOH . D 4 HOH X 38 528 528 HOH HOH . D 4 HOH X 39 529 529 HOH HOH . D 4 HOH X 40 530 530 HOH HOH . D 4 HOH X 41 531 531 HOH HOH . D 4 HOH X 42 532 532 HOH HOH . D 4 HOH X 43 533 533 HOH HOH . D 4 HOH X 44 534 534 HOH HOH . D 4 HOH X 45 535 535 HOH HOH . D 4 HOH X 46 536 536 HOH HOH . D 4 HOH X 47 537 537 HOH HOH . D 4 HOH X 48 538 538 HOH HOH . D 4 HOH X 49 539 539 HOH HOH . D 4 HOH X 50 540 540 HOH HOH . D 4 HOH X 51 541 541 HOH HOH . D 4 HOH X 52 542 542 HOH HOH . D 4 HOH X 53 543 543 HOH HOH . D 4 HOH X 54 544 544 HOH HOH . D 4 HOH X 55 545 545 HOH HOH . D 4 HOH X 56 546 546 HOH HOH . D 4 HOH X 57 547 547 HOH HOH . D 4 HOH X 58 548 548 HOH HOH . D 4 HOH X 59 549 549 HOH HOH . D 4 HOH X 60 550 550 HOH HOH . D 4 HOH X 61 551 551 HOH HOH . D 4 HOH X 62 552 552 HOH HOH . D 4 HOH X 63 553 553 HOH HOH . D 4 HOH X 64 554 554 HOH HOH . D 4 HOH X 65 555 555 HOH HOH . D 4 HOH X 66 556 556 HOH HOH . D 4 HOH X 67 557 557 HOH HOH . D 4 HOH X 68 558 558 HOH HOH . D 4 HOH X 69 559 559 HOH HOH . D 4 HOH X 70 560 560 HOH HOH . D 4 HOH X 71 561 561 HOH HOH . D 4 HOH X 72 562 562 HOH HOH . D 4 HOH X 73 563 563 HOH HOH . D 4 HOH X 74 564 564 HOH HOH . D 4 HOH X 75 565 565 HOH HOH . D 4 HOH X 76 566 566 HOH HOH . D 4 HOH X 77 567 567 HOH HOH . D 4 HOH X 78 568 568 HOH HOH . D 4 HOH X 79 569 569 HOH HOH . D 4 HOH X 80 570 570 HOH HOH . D 4 HOH X 81 571 571 HOH HOH . D 4 HOH X 82 572 572 HOH HOH . D 4 HOH X 83 573 573 HOH HOH . D 4 HOH X 84 574 574 HOH HOH . D 4 HOH X 85 575 575 HOH HOH . D 4 HOH X 86 576 576 HOH HOH . D 4 HOH X 87 577 577 HOH HOH . D 4 HOH X 88 578 578 HOH HOH . D 4 HOH X 89 579 579 HOH HOH . D 4 HOH X 90 580 580 HOH HOH . D 4 HOH X 91 581 581 HOH HOH . D 4 HOH X 92 582 582 HOH HOH . D 4 HOH X 93 583 583 HOH HOH . D 4 HOH X 94 584 584 HOH HOH . D 4 HOH X 95 585 585 HOH HOH . D 4 HOH X 96 586 586 HOH HOH . D 4 HOH X 97 587 587 HOH HOH . D 4 HOH X 98 588 588 HOH HOH . D 4 HOH X 99 589 589 HOH HOH . D 4 HOH X 100 590 590 HOH HOH . D 4 HOH X 101 591 591 HOH HOH . D 4 HOH X 102 592 592 HOH HOH . D 4 HOH X 103 593 593 HOH HOH . D 4 HOH X 104 594 594 HOH HOH . D 4 HOH X 105 595 595 HOH HOH . D 4 HOH X 106 596 596 HOH HOH . D 4 HOH X 107 597 597 HOH HOH . D 4 HOH X 108 598 598 HOH HOH . D 4 HOH X 109 599 599 HOH HOH . D 4 HOH X 110 600 600 HOH HOH . D 4 HOH X 111 601 601 HOH HOH . D 4 HOH X 112 602 602 HOH HOH . D 4 HOH X 113 603 603 HOH HOH . D 4 HOH X 114 604 604 HOH HOH . D 4 HOH X 115 605 605 HOH HOH . D 4 HOH X 116 606 606 HOH HOH . D 4 HOH X 117 607 607 HOH HOH . D 4 HOH X 118 608 608 HOH HOH . D 4 HOH X 119 609 609 HOH HOH . D 4 HOH X 120 610 610 HOH HOH . D 4 HOH X 121 611 611 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 PA NAP . . . C 3 111.616 18.66 51.152 1 81.43 ? PA NAP 490 X 1 HETATM 2 O O1A NAP . . . C 3 112.536 19.544 51.932 1 80.69 ? O1A NAP 490 X 1 HETATM 3 O O2A NAP . . . C 3 110.55 19.446 50.482 1 80.89 ? O2A NAP 490 X 1 HETATM 4 O O5B NAP . . . C 3 112.494 17.883 50.046 1 78.05 ? O5B NAP 490 X 1 HETATM 5 C C5B NAP . . . C 3 113.296 16.764 50.361 1 73.43 ? C5B NAP 490 X 1 HETATM 6 C C4B NAP . . . C 3 113.861 16.195 49.064 1 70.59 ? C4B NAP 490 X 1 HETATM 7 O O4B NAP . . . C 3 114.637 15.038 49.32 1 69.43 ? O4B NAP 490 X 1 HETATM 8 C C3B NAP . . . C 3 112.764 15.778 48.099 1 69.36 ? C3B NAP 490 X 1 HETATM 9 O O3B NAP . . . C 3 113.148 16.189 46.804 1 69 ? O3B NAP 490 X 1 HETATM 10 C C2B NAP . . . C 3 112.702 14.267 48.23 1 68.14 ? C2B NAP 490 X 1 HETATM 11 O O2B NAP . . . C 3 112.428 13.612 47.015 1 67.32 ? O2B NAP 490 X 1 HETATM 12 C C1B NAP . . . C 3 114.092 13.889 48.692 1 67.04 ? C1B NAP 490 X 1 HETATM 13 N N9A NAP . . . C 3 114.067 12.762 49.638 1 66 ? N9A NAP 490 X 1 HETATM 14 C C8A NAP . . . C 3 113.194 12.557 50.679 1 65.77 ? C8A NAP 490 X 1 HETATM 15 N N7A NAP . . . C 3 113.533 11.403 51.304 1 65.47 ? N7A NAP 490 X 1 HETATM 16 C C5A NAP . . . C 3 114.612 10.878 50.677 1 65.46 ? C5A NAP 490 X 1 HETATM 17 C C6A NAP . . . C 3 115.362 9.729 50.911 1 65.67 ? C6A NAP 490 X 1 HETATM 18 N N6A NAP . . . C 3 115.303 9.166 52.116 1 64.47 ? N6A NAP 490 X 1 HETATM 19 N N1A NAP . . . C 3 116.437 9.449 50.083 1 65.51 ? N1A NAP 490 X 1 HETATM 20 C C2A NAP . . . C 3 116.767 10.299 49.04 1 65.89 ? C2A NAP 490 X 1 HETATM 21 N N3A NAP . . . C 3 116.021 11.442 48.82 1 65.45 ? N3A NAP 490 X 1 HETATM 22 C C4A NAP . . . C 3 114.959 11.722 49.626 1 65.67 ? C4A NAP 490 X 1 HETATM 23 O O3 NAP . . . C 3 111.01 17.443 52.043 1 84.24 ? O3 NAP 490 X 1 HETATM 24 P PN NAP . . . C 3 109.697 17.491 52.997 1 87.79 ? PN NAP 490 X 1 HETATM 25 O O1N NAP . . . C 3 109.265 16.09 53.241 1 88.04 ? O1N NAP 490 X 1 HETATM 26 O O2N NAP . . . C 3 109.975 18.367 54.165 1 87.01 ? O2N NAP 490 X 1 HETATM 27 O O5D NAP . . . C 3 108.558 18.174 52.08 1 89.76 ? O5D NAP 490 X 1 HETATM 28 C C5D NAP . . . C 3 107.227 18.325 52.543 1 92.66 ? C5D NAP 490 X 1 HETATM 29 C C4D NAP . . . C 3 106.244 18.108 51.393 1 94.6 ? C4D NAP 490 X 1 HETATM 30 O O4D NAP . . . C 3 106.653 18.82 50.23 1 95.28 ? O4D NAP 490 X 1 HETATM 31 C C3D NAP . . . C 3 106.137 16.631 51.024 1 95.36 ? C3D NAP 490 X 1 HETATM 32 O O3D NAP . . . C 3 104.868 16.127 51.39 1 95.58 ? O3D NAP 490 X 1 HETATM 33 C C2D NAP . . . C 3 106.37 16.57 49.522 1 95.53 ? C2D NAP 490 X 1 HETATM 34 O O2D NAP . . . C 3 105.17 16.29 48.836 1 95.76 ? O2D NAP 490 X 1 HETATM 35 C C1D NAP . . . C 3 106.861 17.957 49.121 1 95.52 ? C1D NAP 490 X 1 HETATM 36 P P2B NAP . . . C 3 110.998 12.933 46.732 1 65.62 ? P2B NAP 490 X 1 HETATM 37 O O1X NAP . . . C 3 110.132 12.876 47.965 1 65.69 ? O1X NAP 490 X 1 HETATM 38 O O2X NAP . . . C 3 111.241 11.517 46.283 1 67.53 ? O2X NAP 490 X 1 HETATM 39 O O3X NAP . . . C 3 110.31 13.729 45.654 1 66.14 ? O3X NAP 490 X 1 # _model_server_stats.io_time_ms 4 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #