data_6KDU # _model_server_result.job_id 08Jss0IR_Lhd0RAkO4-UMw _model_server_result.datetime_utc '2025-08-31 21:11:47' _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 6kdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 6KDU # _exptl.entry_id 6KDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 335.227 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE' _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 6KDU _cell.length_a 96.168 _cell.length_b 96.168 _cell.length_c 200.835 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,G _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 # _chem_comp.formula 'C11 H16 N2 O8 P 1' _chem_comp.formula_weight 335.227 _chem_comp.id NMN _chem_comp.mon_nstd_flag . _chem_comp.name 'BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'NICOTINAMIDE MONONUCLEOTIDE' # 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 O3P P NMN doub 276 n n P O1P NMN sing 277 n n P O2P NMN sing 278 n n P O5R NMN sing 279 n n O1P H1PO NMN sing 280 n n O2P H2PO NMN sing 281 n n O5R C5R NMN sing 282 n n C5R C4R NMN sing 283 n n C5R H5R1 NMN sing 284 n n C5R H5R2 NMN sing 285 n n C4R O4R NMN sing 286 n n C4R C3R NMN sing 287 n n C4R H4RC NMN sing 288 n n O4R C1R NMN sing 289 n n C3R O3R NMN sing 290 n n C3R C2R NMN sing 291 n n C3R H3RC NMN sing 292 n n O3R H3RO NMN sing 293 n n C2R O2R NMN sing 294 n n C2R C1R NMN sing 295 n n C2R H2RC NMN sing 296 n n O2R H2RO NMN sing 297 n n C1R N1 NMN sing 298 n n C1R H1RC NMN sing 299 n n N1 C2 NMN doub 300 n y N1 C6 NMN sing 301 n y C2 C3 NMN sing 302 n y C2 HC2 NMN sing 303 n n C3 C7 NMN sing 304 n n C3 C4 NMN doub 305 n y C7 O7 NMN doub 306 n n C7 N7 NMN sing 307 n n N7 HN71 NMN sing 308 n n N7 HN72 NMN sing 309 n n C4 C5 NMN sing 310 n y C4 HC4 NMN sing 311 n n C5 C6 NMN doub 312 n y C5 HC5 NMN sing 313 n n C6 HC6 NMN sing 314 n n # _atom_sites.entry_id 6KDU _atom_sites.fract_transf_matrix[1][1] 0.010398 _atom_sites.fract_transf_matrix[1][2] 0.006004 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012007 _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] 0.004979 _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 AMP A 1 401 1 AMP AMP . C 3 NMN A 1 402 2 NMN LIG . D 4 SO4 A 1 403 2 SO4 SO4 . E 4 SO4 A 1 404 3 SO4 SO4 . F 4 SO4 A 1 405 4 SO4 SO4 . G 5 HOH A 1 501 47 HOH HOH . G 5 HOH A 2 502 51 HOH HOH . G 5 HOH A 3 503 31 HOH HOH . G 5 HOH A 4 504 118 HOH HOH . G 5 HOH A 5 505 16 HOH HOH . G 5 HOH A 6 506 21 HOH HOH . G 5 HOH A 7 507 70 HOH HOH . G 5 HOH A 8 508 23 HOH HOH . G 5 HOH A 9 509 99 HOH HOH . G 5 HOH A 10 510 20 HOH HOH . G 5 HOH A 11 511 43 HOH HOH . G 5 HOH A 12 512 50 HOH HOH . G 5 HOH A 13 513 32 HOH HOH . G 5 HOH A 14 514 156 HOH HOH . G 5 HOH A 15 515 144 HOH HOH . G 5 HOH A 16 516 54 HOH HOH . G 5 HOH A 17 517 68 HOH HOH . G 5 HOH A 18 518 49 HOH HOH . G 5 HOH A 19 519 36 HOH HOH . G 5 HOH A 20 520 5 HOH HOH . G 5 HOH A 21 521 17 HOH HOH . G 5 HOH A 22 522 14 HOH HOH . G 5 HOH A 23 523 193 HOH HOH . G 5 HOH A 24 524 10 HOH HOH . G 5 HOH A 25 525 188 HOH HOH . G 5 HOH A 26 526 40 HOH HOH . G 5 HOH A 27 527 15 HOH HOH . G 5 HOH A 28 528 11 HOH HOH . G 5 HOH A 29 529 38 HOH HOH . G 5 HOH A 30 530 121 HOH HOH . G 5 HOH A 31 531 96 HOH HOH . G 5 HOH A 32 532 110 HOH HOH . G 5 HOH A 33 533 27 HOH HOH . G 5 HOH A 34 534 4 HOH HOH . G 5 HOH A 35 535 124 HOH HOH . G 5 HOH A 36 536 19 HOH HOH . G 5 HOH A 37 537 63 HOH HOH . G 5 HOH A 38 538 85 HOH HOH . G 5 HOH A 39 539 28 HOH HOH . G 5 HOH A 40 540 56 HOH HOH . G 5 HOH A 41 541 154 HOH HOH . G 5 HOH A 42 542 44 HOH HOH . G 5 HOH A 43 543 46 HOH HOH . G 5 HOH A 44 544 133 HOH HOH . G 5 HOH A 45 545 102 HOH HOH . G 5 HOH A 46 546 136 HOH HOH . G 5 HOH A 47 547 37 HOH HOH . G 5 HOH A 48 548 97 HOH HOH . G 5 HOH A 49 549 115 HOH HOH . G 5 HOH A 50 550 8 HOH HOH . G 5 HOH A 51 551 69 HOH HOH . G 5 HOH A 52 552 53 HOH HOH . G 5 HOH A 53 553 134 HOH HOH . G 5 HOH A 54 554 42 HOH HOH . G 5 HOH A 55 555 34 HOH HOH . G 5 HOH A 56 556 45 HOH HOH . G 5 HOH A 57 557 6 HOH HOH . G 5 HOH A 58 558 159 HOH HOH . G 5 HOH A 59 559 66 HOH HOH . G 5 HOH A 60 560 33 HOH HOH . G 5 HOH A 61 561 86 HOH HOH . G 5 HOH A 62 562 48 HOH HOH . G 5 HOH A 63 563 61 HOH HOH . G 5 HOH A 64 564 12 HOH HOH . G 5 HOH A 65 565 64 HOH HOH . G 5 HOH A 66 566 83 HOH HOH . G 5 HOH A 67 567 157 HOH HOH . G 5 HOH A 68 568 94 HOH HOH . G 5 HOH A 69 569 84 HOH HOH . G 5 HOH A 70 570 79 HOH HOH . G 5 HOH A 71 571 74 HOH HOH . G 5 HOH A 72 572 131 HOH HOH . G 5 HOH A 73 573 101 HOH HOH . G 5 HOH A 74 574 3 HOH HOH . G 5 HOH A 75 575 41 HOH HOH . G 5 HOH A 76 576 25 HOH HOH . G 5 HOH A 77 577 73 HOH HOH . G 5 HOH A 78 578 29 HOH HOH . G 5 HOH A 79 579 92 HOH HOH . G 5 HOH A 80 580 130 HOH HOH . G 5 HOH A 81 581 35 HOH HOH . G 5 HOH A 82 582 191 HOH HOH . G 5 HOH A 83 583 1 HOH HOH . G 5 HOH A 84 584 78 HOH HOH . G 5 HOH A 85 585 167 HOH HOH . G 5 HOH A 86 586 185 HOH HOH . G 5 HOH A 87 587 175 HOH HOH . G 5 HOH A 88 588 141 HOH HOH . G 5 HOH A 89 589 76 HOH HOH . G 5 HOH A 90 590 132 HOH HOH . G 5 HOH A 91 591 186 HOH HOH . G 5 HOH A 92 592 125 HOH HOH . G 5 HOH A 93 593 146 HOH HOH . G 5 HOH A 94 594 91 HOH HOH . G 5 HOH A 95 595 30 HOH HOH . G 5 HOH A 96 596 71 HOH HOH . G 5 HOH A 97 597 142 HOH HOH . G 5 HOH A 98 598 192 HOH HOH . G 5 HOH A 99 599 72 HOH HOH . G 5 HOH A 100 600 129 HOH HOH . G 5 HOH A 101 601 57 HOH HOH . G 5 HOH A 102 602 190 HOH HOH . G 5 HOH A 103 603 114 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 O O3P NMN . . . C 3 19.612 18.358 88.567 1 114.52 ? O3P NMN 402 A 1 HETATM 2 P P NMN . . . C 3 19.428 19.48 89.603 1 138.66 ? P NMN 402 A 1 HETATM 3 O O1P NMN . . . C 3 20.646 20.339 89.801 1 117.62 ? O1P NMN 402 A 1 HETATM 4 O O2P NMN . . . C 3 18.504 19.194 90.717 1 115.13 ? O2P NMN 402 A 1 HETATM 5 O O5R NMN . . . C 3 18.46 20.527 88.579 1 98.12 ? O5R NMN 402 A 1 HETATM 6 C C5R NMN . . . C 3 19.044 21.494 88.034 1 81.54 ? C5R NMN 402 A 1 HETATM 7 C C4R NMN . . . C 3 19.297 20.981 86.432 1 73.62 ? C4R NMN 402 A 1 HETATM 8 O O4R NMN . . . C 3 18.718 21.875 85.594 1 54.77 ? O4R NMN 402 A 1 HETATM 9 C C3R NMN . . . C 3 20.741 20.94 86.146 1 74.07 ? C3R NMN 402 A 1 HETATM 10 O O3R NMN . . . C 3 21.022 20.095 85.141 1 74.09 ? O3R NMN 402 A 1 HETATM 11 C C2R NMN . . . C 3 20.958 22.333 85.672 1 66.41 ? C2R NMN 402 A 1 HETATM 12 O O2R NMN . . . C 3 22.054 22.489 84.855 1 59.95 ? O2R NMN 402 A 1 HETATM 13 C C1R NMN . . . C 3 19.7 22.364 84.788 1 62.44 ? C1R NMN 402 A 1 HETATM 14 N N1 NMN . . . C 3 19.302 23.711 84.454 1 50.02 ? N1 NMN 402 A 1 HETATM 15 C C2 NMN . . . C 3 19.706 24.142 83.273 1 53.27 ? C2 NMN 402 A 1 HETATM 16 C C3 NMN . . . C 3 19.422 25.394 82.817 1 50.91 ? C3 NMN 402 A 1 HETATM 17 C C7 NMN . . . C 3 19.874 25.822 81.522 1 49.62 ? C7 NMN 402 A 1 HETATM 18 O O7 NMN . . . C 3 19.513 26.924 81.123 1 48.85 ? O7 NMN 402 A 1 HETATM 19 N N7 NMN . . . C 3 20.649 25.126 80.669 1 55.16 ? N7 NMN 402 A 1 HETATM 20 C C4 NMN . . . C 3 18.698 26.196 83.659 1 48.57 ? C4 NMN 402 A 1 HETATM 21 C C5 NMN . . . C 3 18.273 25.746 84.885 1 46.07 ? C5 NMN 402 A 1 HETATM 22 C C6 NMN . . . C 3 18.584 24.482 85.268 1 54.91 ? C6 NMN 402 A 1 HETATM 23 H H5R1 NMN . . . C 3 19.979 21.661 88.23 1 97.85 ? H5R1 NMN 402 A 1 HETATM 24 H H5R2 NMN . . . C 3 18.557 22.322 87.893 1 97.85 ? H5R2 NMN 402 A 1 HETATM 25 H H4RC NMN . . . C 3 18.822 20.136 86.402 1 88.34 ? H4RC NMN 402 A 1 HETATM 26 H H3RC NMN . . . C 3 21.276 20.825 86.947 1 88.89 ? H3RC NMN 402 A 1 HETATM 27 H H3RO NMN . . . C 3 20.616 19.361 85.277 1 88.91 ? H3RO NMN 402 A 1 HETATM 28 H H2RC NMN . . . C 3 20.909 22.984 86.39 1 79.69 ? H2RC NMN 402 A 1 HETATM 29 H H2RO NMN . . . C 3 22.203 23.325 84.814 1 71.94 ? H2RO NMN 402 A 1 HETATM 30 H H1RC NMN . . . C 3 19.833 21.878 83.96 1 74.92 ? H1RC NMN 402 A 1 HETATM 31 H HC2 NMN . . . C 3 20.197 23.524 82.782 1 63.92 ? HC2 NMN 402 A 1 HETATM 32 H HN71 NMN . . . C 3 20.975 24.343 80.807 1 66.19 ? HN71 NMN 402 A 1 HETATM 33 H HN72 NMN . . . C 3 20.872 25.458 79.907 1 66.19 ? HN72 NMN 402 A 1 HETATM 34 H HC4 NMN . . . C 3 18.46 27.058 83.405 1 58.29 ? HC4 NMN 402 A 1 HETATM 35 H HC5 NMN . . . C 3 17.774 26.288 85.454 1 55.28 ? HC5 NMN 402 A 1 HETATM 36 H HC6 NMN . . . C 3 18.333 24.14 86.095 1 65.89 ? HC6 NMN 402 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 387 _model_server_stats.encode_time_ms 51 _model_server_stats.element_count 36 #