data_1BDB # _model_server_result.job_id jfLYhwxvBEdKlRG8lqeM8A _model_server_result.datetime_utc '2025-06-22 13:55:55' _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 1bdb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 1BDB # _exptl.entry_id 1BDB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 1BDB _cell.length_a 79.2 _cell.length_b 79.2 _cell.length_c 152.88 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BDB _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 4_775 -x+2,-y+2,z -1 0 0 0 -1 0 0 0 1 79.2 137.178424 0 3 'crystal symmetry operation' 8_675 x-y+1,-y+2,-z 1 0 0 0 -1 0 0 0 -1 0 137.178424 0 4 'crystal symmetry operation' 11_655 -x+y+1,y,-z -1 0 0 0 1 0 0 0 -1 79.2 0 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 # _chem_comp.formula 'C21 H27 N7 O14 P2' _chem_comp.formula_weight 663.425 _chem_comp.id NAD _chem_comp.mon_nstd_flag . _chem_comp.name NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 PA O1A NAD doub 237 n n PA O2A NAD sing 238 n n PA O5B NAD sing 239 n n PA O3 NAD sing 240 n n O2A HOA2 NAD sing 241 n n O5B C5B NAD sing 242 n n C5B C4B NAD sing 243 n n C5B H51A NAD sing 244 n n C5B H52A NAD sing 245 n n C4B O4B NAD sing 246 n n C4B C3B NAD sing 247 n n C4B H4B NAD sing 248 n n O4B C1B NAD sing 249 n n C3B O3B NAD sing 250 n n C3B C2B NAD sing 251 n n C3B H3B NAD sing 252 n n O3B HO3A NAD sing 253 n n C2B O2B NAD sing 254 n n C2B C1B NAD sing 255 n n C2B H2B NAD sing 256 n n O2B HO2A NAD sing 257 n n C1B N9A NAD sing 258 n n C1B H1B NAD sing 259 n n N9A C8A NAD sing 260 n y N9A C4A NAD sing 261 n y C8A N7A NAD doub 262 n y C8A H8A NAD sing 263 n n N7A C5A NAD sing 264 n y C5A C6A NAD sing 265 n y C5A C4A NAD doub 266 n y C6A N6A NAD sing 267 n n C6A N1A NAD doub 268 n y N6A H61A NAD sing 269 n n N6A H62A NAD sing 270 n n N1A C2A NAD sing 271 n y C2A N3A NAD doub 272 n y C2A H2A NAD sing 273 n n N3A C4A NAD sing 274 n y O3 PN NAD sing 275 n n PN O1N NAD doub 276 n n PN O2N NAD sing 277 n n PN O5D NAD sing 278 n n O5D C5D NAD sing 279 n n C5D C4D NAD sing 280 n n C5D H51N NAD sing 281 n n C5D H52N NAD sing 282 n n C4D O4D NAD sing 283 n n C4D C3D NAD sing 284 n n C4D H4D NAD sing 285 n n O4D C1D NAD sing 286 n n C3D O3D NAD sing 287 n n C3D C2D NAD sing 288 n n C3D H3D NAD sing 289 n n O3D HO3N NAD sing 290 n n C2D O2D NAD sing 291 n n C2D C1D NAD sing 292 n n C2D H2D NAD sing 293 n n O2D HO2N NAD sing 294 n n C1D N1N NAD sing 295 n n C1D H1D NAD sing 296 n n N1N C2N NAD sing 297 n y N1N C6N NAD doub 298 n y C2N C3N NAD doub 299 n y C2N H2N NAD sing 300 n n C3N C7N NAD sing 301 n n C3N C4N NAD sing 302 n y C7N O7N NAD doub 303 n n C7N N7N NAD sing 304 n n N7N H71N NAD sing 305 n n N7N H72N NAD sing 306 n n C4N C5N NAD doub 307 n y C4N H4N NAD sing 308 n n C5N C6N NAD sing 309 n y C5N H5N NAD sing 310 n n C6N H6N NAD sing 311 n n # _atom_sites.entry_id 1BDB _atom_sites.fract_transf_matrix[1][1] 0.012626 _atom_sites.fract_transf_matrix[1][2] 0.00729 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01458 _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] 0.006541 _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 NAD A 1 300 300 NAD NAD . C 3 HOH A 1 500 500 HOH HOH . C 3 HOH A 2 501 501 HOH HOH . C 3 HOH A 3 502 502 HOH HOH . C 3 HOH A 4 503 503 HOH HOH . C 3 HOH A 5 504 504 HOH HOH . C 3 HOH A 6 505 505 HOH HOH . C 3 HOH A 7 506 506 HOH HOH . C 3 HOH A 8 507 507 HOH HOH . C 3 HOH A 9 508 508 HOH HOH . C 3 HOH A 10 509 509 HOH HOH . C 3 HOH A 11 510 510 HOH HOH . C 3 HOH A 12 511 511 HOH HOH . C 3 HOH A 13 512 512 HOH HOH . C 3 HOH A 14 513 513 HOH HOH . C 3 HOH A 15 514 514 HOH HOH . C 3 HOH A 16 515 515 HOH HOH . C 3 HOH A 17 516 516 HOH HOH . C 3 HOH A 18 517 517 HOH HOH . C 3 HOH A 19 518 518 HOH HOH . C 3 HOH A 20 519 519 HOH HOH . C 3 HOH A 21 520 520 HOH HOH . C 3 HOH A 22 521 521 HOH HOH . C 3 HOH A 23 522 522 HOH HOH . C 3 HOH A 24 523 523 HOH HOH . C 3 HOH A 25 524 524 HOH HOH . C 3 HOH A 26 525 525 HOH HOH . C 3 HOH A 27 526 526 HOH HOH . C 3 HOH A 28 527 527 HOH HOH . C 3 HOH A 29 528 528 HOH HOH . C 3 HOH A 30 529 529 HOH HOH . C 3 HOH A 31 530 530 HOH HOH . C 3 HOH A 32 531 531 HOH HOH . C 3 HOH A 33 532 532 HOH HOH . C 3 HOH A 34 533 533 HOH HOH . C 3 HOH A 35 534 534 HOH HOH . C 3 HOH A 36 535 535 HOH HOH . C 3 HOH A 37 536 536 HOH HOH . C 3 HOH A 38 537 537 HOH HOH . C 3 HOH A 39 538 538 HOH HOH . C 3 HOH A 40 539 539 HOH HOH . C 3 HOH A 41 540 540 HOH HOH . C 3 HOH A 42 541 541 HOH HOH . C 3 HOH A 43 542 542 HOH HOH . C 3 HOH A 44 543 543 HOH HOH . C 3 HOH A 45 544 544 HOH HOH . C 3 HOH A 46 545 545 HOH HOH . C 3 HOH A 47 546 546 HOH HOH . C 3 HOH A 48 547 547 HOH HOH . C 3 HOH A 49 548 548 HOH HOH . C 3 HOH A 50 549 549 HOH HOH . C 3 HOH A 51 550 550 HOH HOH . C 3 HOH A 52 551 551 HOH HOH . C 3 HOH A 53 552 552 HOH HOH . C 3 HOH A 54 553 553 HOH HOH . C 3 HOH A 55 554 554 HOH HOH . C 3 HOH A 56 555 555 HOH HOH . C 3 HOH A 57 556 556 HOH HOH . C 3 HOH A 58 557 557 HOH HOH . C 3 HOH A 59 558 558 HOH HOH . C 3 HOH A 60 559 559 HOH HOH . C 3 HOH A 61 560 560 HOH HOH . C 3 HOH A 62 561 561 HOH HOH . C 3 HOH A 63 562 562 HOH HOH . C 3 HOH A 64 563 563 HOH HOH . C 3 HOH A 65 564 564 HOH HOH . C 3 HOH A 66 565 565 HOH HOH . C 3 HOH A 67 566 566 HOH HOH . C 3 HOH A 68 567 567 HOH HOH . C 3 HOH A 69 568 568 HOH HOH . C 3 HOH A 70 569 569 HOH HOH . C 3 HOH A 71 570 570 HOH HOH . C 3 HOH A 72 571 571 HOH HOH . C 3 HOH A 73 572 572 HOH HOH . C 3 HOH A 74 573 573 HOH HOH . C 3 HOH A 75 574 574 HOH HOH . C 3 HOH A 76 575 575 HOH HOH . C 3 HOH A 77 576 576 HOH HOH . C 3 HOH A 78 577 577 HOH HOH . C 3 HOH A 79 578 578 HOH HOH . C 3 HOH A 80 579 579 HOH HOH . C 3 HOH A 81 580 580 HOH HOH . C 3 HOH A 82 581 581 HOH HOH . C 3 HOH A 83 582 582 HOH HOH . C 3 HOH A 84 583 583 HOH HOH . C 3 HOH A 85 584 584 HOH HOH . C 3 HOH A 86 585 585 HOH HOH . C 3 HOH A 87 586 586 HOH HOH . C 3 HOH A 88 587 587 HOH HOH . C 3 HOH A 89 588 588 HOH HOH . C 3 HOH A 90 589 589 HOH HOH . C 3 HOH A 91 590 590 HOH HOH . C 3 HOH A 92 591 591 HOH HOH . C 3 HOH A 93 592 592 HOH HOH . C 3 HOH A 94 593 593 HOH HOH . C 3 HOH A 95 594 594 HOH HOH . C 3 HOH A 96 595 595 HOH HOH . C 3 HOH A 97 597 597 HOH HOH . C 3 HOH A 98 598 598 HOH HOH . C 3 HOH A 99 599 599 HOH HOH . C 3 HOH A 100 600 600 HOH HOH . C 3 HOH A 101 601 601 HOH HOH . C 3 HOH A 102 602 602 HOH HOH . C 3 HOH A 103 603 603 HOH HOH . C 3 HOH A 104 604 604 HOH HOH . C 3 HOH A 105 605 605 HOH HOH . C 3 HOH A 106 606 606 HOH HOH . C 3 HOH A 107 607 607 HOH HOH . C 3 HOH A 108 608 608 HOH HOH . C 3 HOH A 109 609 609 HOH HOH . C 3 HOH A 110 610 610 HOH HOH . C 3 HOH A 111 611 611 HOH HOH . C 3 HOH A 112 612 612 HOH HOH . C 3 HOH A 113 613 613 HOH HOH . C 3 HOH A 114 614 614 HOH HOH . C 3 HOH A 115 615 615 HOH HOH . C 3 HOH A 116 616 616 HOH HOH . C 3 HOH A 117 617 617 HOH HOH . C 3 HOH A 118 618 618 HOH HOH . C 3 HOH A 119 619 619 HOH HOH . C 3 HOH A 120 620 620 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 NAD . . . B 2 23.06 48.605 11.355 1 26.45 ? PA NAD 300 A 1 HETATM 2 O O1A NAD . . . B 2 23.854 47.461 11.86 1 27.16 ? O1A NAD 300 A 1 HETATM 3 O O2A NAD . . . B 2 21.915 48.905 12.237 1 27 ? O2A NAD 300 A 1 HETATM 4 O O5B NAD . . . B 2 22.509 48.297 9.903 1 25.56 ? O5B NAD 300 A 1 HETATM 5 C C5B NAD . . . B 2 23.293 47.456 8.997 1 22.97 ? C5B NAD 300 A 1 HETATM 6 C C4B NAD . . . B 2 22.245 46.674 8.177 1 20.73 ? C4B NAD 300 A 1 HETATM 7 O O4B NAD . . . B 2 23.063 45.998 7.175 1 18.24 ? O4B NAD 300 A 1 HETATM 8 C C3B NAD . . . B 2 21.57 45.586 9.029 1 18.82 ? C3B NAD 300 A 1 HETATM 9 O O3B NAD . . . B 2 20.178 45.45 8.778 1 18.97 ? O3B NAD 300 A 1 HETATM 10 C C2B NAD . . . B 2 22.361 44.338 8.653 1 18.45 ? C2B NAD 300 A 1 HETATM 11 O O2B NAD . . . B 2 21.655 43.108 8.786 1 16 ? O2B NAD 300 A 1 HETATM 12 C C1B NAD . . . B 2 22.67 44.641 7.162 1 17.97 ? C1B NAD 300 A 1 HETATM 13 N N9A NAD . . . B 2 23.87 43.892 6.746 1 17.14 ? N9A NAD 300 A 1 HETATM 14 C C8A NAD . . . B 2 25.065 43.774 7.398 1 17.39 ? C8A NAD 300 A 1 HETATM 15 N N7A NAD . . . B 2 25.931 43.002 6.738 1 18.09 ? N7A NAD 300 A 1 HETATM 16 C C5A NAD . . . B 2 25.235 42.587 5.632 1 15.87 ? C5A NAD 300 A 1 HETATM 17 C C6A NAD . . . B 2 25.593 41.758 4.565 1 15.23 ? C6A NAD 300 A 1 HETATM 18 N N6A NAD . . . B 2 26.796 41.172 4.472 1 15.37 ? N6A NAD 300 A 1 HETATM 19 N N1A NAD . . . B 2 24.65 41.567 3.613 1 14.19 ? N1A NAD 300 A 1 HETATM 20 C C2A NAD . . . B 2 23.423 42.168 3.721 1 13.29 ? C2A NAD 300 A 1 HETATM 21 N N3A NAD . . . B 2 23.003 42.945 4.666 1 14.38 ? N3A NAD 300 A 1 HETATM 22 C C4A NAD . . . B 2 23.957 43.119 5.611 1 16.9 ? C4A NAD 300 A 1 HETATM 23 O O3 NAD . . . B 2 24.046 49.825 11.079 1 28.93 ? O3 NAD 300 A 1 HETATM 24 P PN NAD . . . B 2 23.908 51.329 10.566 1 29.93 ? PN NAD 300 A 1 HETATM 25 O O1N NAD . . . B 2 24.309 52.198 11.685 1 32.33 ? O1N NAD 300 A 1 HETATM 26 O O2N NAD . . . B 2 22.553 51.67 10.127 1 29.47 ? O2N NAD 300 A 1 HETATM 27 O O5D NAD . . . B 2 24.946 51.345 9.343 1 31.48 ? O5D NAD 300 A 1 HETATM 28 C C5D NAD . . . B 2 24.384 51.755 8.061 1 32.48 ? C5D NAD 300 A 1 HETATM 29 C C4D NAD . . . B 2 25.461 52.467 7.274 1 32.8 ? C4D NAD 300 A 1 HETATM 30 O O4D NAD . . . B 2 25.739 53.678 8.033 1 34.84 ? O4D NAD 300 A 1 HETATM 31 C C3D NAD . . . B 2 26.782 51.692 7.175 1 32.97 ? C3D NAD 300 A 1 HETATM 32 O O3D NAD . . . B 2 27.418 51.908 5.925 1 31.12 ? O3D NAD 300 A 1 HETATM 33 C C2D NAD . . . B 2 27.616 52.295 8.312 1 34.21 ? C2D NAD 300 A 1 HETATM 34 O O2D NAD . . . B 2 29.004 52.159 7.981 1 35.09 ? O2D NAD 300 A 1 HETATM 35 C C1D NAD . . . B 2 27.14 53.742 8.251 1 35.62 ? C1D NAD 300 A 1 HETATM 36 N N1N NAD . . . B 2 27.388 54.573 9.418 1 37.25 ? N1N NAD 300 A 1 HETATM 37 C C2N NAD . . . B 2 26.992 54.171 10.651 1 37.93 ? C2N NAD 300 A 1 HETATM 38 C C3N NAD . . . B 2 27.281 54.958 11.734 1 38.36 ? C3N NAD 300 A 1 HETATM 39 C C7N NAD . . . B 2 26.924 54.685 13.233 1 38.93 ? C7N NAD 300 A 1 HETATM 40 O O7N NAD . . . B 2 27.483 55.385 14.084 1 38.57 ? O7N NAD 300 A 1 HETATM 41 N N7N NAD . . . B 2 26.019 53.731 13.484 1 38.42 ? N7N NAD 300 A 1 HETATM 42 C C4N NAD . . . B 2 27.965 56.198 11.636 1 38.07 ? C4N NAD 300 A 1 HETATM 43 C C5N NAD . . . B 2 28.252 56.558 10.324 1 38.38 ? C5N NAD 300 A 1 HETATM 44 C C6N NAD . . . B 2 28.003 55.83 9.189 1 37.83 ? C6N NAD 300 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 44 #