data_5YVT # _model_server_result.job_id y4jgWozFYg000QCSioXEDw _model_server_result.datetime_utc '2024-11-05 14:38:24' _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 5yvt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5YVT # _exptl.entry_id 5YVT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 665.441 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' _entity.pdbx_number_of_molecules 2 _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 5YVT _cell.length_a 118.027 _cell.length_b 118.027 _cell.length_c 142.109 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YVT _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N 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 A OD1 ASP 230 A ASP 230 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc2 A OD2 ASP 234 A ASP 234 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc3 C MG MG . A MG 401 1_555 F O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc4 C MG MG . A MG 401 1_555 F O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc5 C MG MG . A MG 401 1_555 B OD2 ASP 215 B ASP 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc6 C MG MG . A MG 401 1_555 G O HOH . B HOH 569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? # _chem_comp.formula 'C21 H29 N7 O14 P2' _chem_comp.formula_weight 665.441 _chem_comp.id NAI _chem_comp.mon_nstd_flag . _chem_comp.name '1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms NADH # 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 NAI doub 237 n n PA O2A NAI sing 238 n n PA O5B NAI sing 239 n n PA O3 NAI sing 240 n n O2A HOA2 NAI sing 241 n n O5B C5B NAI sing 242 n n C5B C4B NAI sing 243 n n C5B H51A NAI sing 244 n n C5B H52A NAI sing 245 n n C4B O4B NAI sing 246 n n C4B C3B NAI sing 247 n n C4B H4B NAI sing 248 n n O4B C1B NAI sing 249 n n C3B O3B NAI sing 250 n n C3B C2B NAI sing 251 n n C3B H3B NAI sing 252 n n O3B HO3A NAI sing 253 n n C2B O2B NAI sing 254 n n C2B C1B NAI sing 255 n n C2B H2B NAI sing 256 n n O2B HO2A NAI sing 257 n n C1B N9A NAI sing 258 n n C1B H1B NAI sing 259 n n N9A C8A NAI sing 260 n y N9A C4A NAI sing 261 n y C8A N7A NAI doub 262 n y C8A H8A NAI sing 263 n n N7A C5A NAI sing 264 n y C5A C6A NAI sing 265 n y C5A C4A NAI doub 266 n y C6A N6A NAI sing 267 n n C6A N1A NAI doub 268 n y N6A H61A NAI sing 269 n n N6A H62A NAI sing 270 n n N1A C2A NAI sing 271 n y C2A N3A NAI doub 272 n y C2A H2A NAI sing 273 n n N3A C4A NAI sing 274 n y O3 PN NAI sing 275 n n PN O1N NAI sing 276 n n PN O2N NAI doub 277 n n PN O5D NAI sing 278 n n O1N HO1N NAI sing 279 n n O5D C5D NAI sing 280 n n C5D C4D NAI sing 281 n n C5D H51N NAI sing 282 n n C5D H52N NAI sing 283 n n C4D O4D NAI sing 284 n n C4D C3D NAI sing 285 n n C4D H4D NAI sing 286 n n O4D C1D NAI sing 287 n n C3D O3D NAI sing 288 n n C3D C2D NAI sing 289 n n C3D H3D NAI sing 290 n n O3D HO3N NAI sing 291 n n C2D O2D NAI sing 292 n n C2D C1D NAI sing 293 n n C2D H2D NAI sing 294 n n O2D HO2N NAI sing 295 n n C1D N1N NAI sing 296 n n C1D H1D NAI sing 297 n n N1N C2N NAI sing 298 n n N1N C6N NAI sing 299 n n C2N C3N NAI doub 300 n n C2N H2N NAI sing 301 n n C3N C7N NAI sing 302 n n C3N C4N NAI sing 303 n n C7N O7N NAI doub 304 n n C7N N7N NAI sing 305 n n N7N H71N NAI sing 306 n n N7N H72N NAI sing 307 n n C4N C5N NAI sing 308 n n C4N H4N NAI sing 309 n n C4N H42N NAI sing 310 n n C5N C6N NAI doub 311 n n C5N H5N NAI sing 312 n n C6N H6N NAI sing 313 n n # _atom_sites.entry_id 5YVT _atom_sites.fract_transf_matrix[1][1] 0.008473 _atom_sites.fract_transf_matrix[1][2] 0.004892 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009783 _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] 0.007037 _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 MG A 1 401 1 MG MG . D 4 NAI A 1 402 1 NAI NAI . E 4 NAI B 1 401 1 NAI NAI . F 5 HOH A 1 501 12 HOH HOH . F 5 HOH A 2 502 47 HOH HOH . F 5 HOH A 3 503 77 HOH HOH . F 5 HOH A 4 504 94 HOH HOH . F 5 HOH A 5 505 7 HOH HOH . F 5 HOH A 6 506 26 HOH HOH . F 5 HOH A 7 507 92 HOH HOH . F 5 HOH A 8 508 49 HOH HOH . F 5 HOH A 9 509 73 HOH HOH . F 5 HOH A 10 510 55 HOH HOH . F 5 HOH A 11 511 70 HOH HOH . F 5 HOH A 12 512 39 HOH HOH . F 5 HOH A 13 513 16 HOH HOH . F 5 HOH A 14 514 67 HOH HOH . F 5 HOH A 15 515 91 HOH HOH . F 5 HOH A 16 516 65 HOH HOH . F 5 HOH A 17 517 80 HOH HOH . G 5 HOH B 1 501 17 HOH HOH . G 5 HOH B 2 502 45 HOH HOH . G 5 HOH B 3 503 75 HOH HOH . G 5 HOH B 4 504 27 HOH HOH . G 5 HOH B 5 505 35 HOH HOH . G 5 HOH B 6 506 19 HOH HOH . G 5 HOH B 7 507 43 HOH HOH . G 5 HOH B 8 508 66 HOH HOH . G 5 HOH B 9 509 30 HOH HOH . G 5 HOH B 10 510 52 HOH HOH . G 5 HOH B 11 511 38 HOH HOH . G 5 HOH B 12 512 5 HOH HOH . G 5 HOH B 13 513 22 HOH HOH . G 5 HOH B 14 514 79 HOH HOH . G 5 HOH B 15 515 2 HOH HOH . G 5 HOH B 16 516 29 HOH HOH . G 5 HOH B 17 517 53 HOH HOH . G 5 HOH B 18 518 6 HOH HOH . G 5 HOH B 19 519 90 HOH HOH . G 5 HOH B 20 520 57 HOH HOH . G 5 HOH B 21 521 15 HOH HOH . G 5 HOH B 22 522 9 HOH HOH . G 5 HOH B 23 523 50 HOH HOH . G 5 HOH B 24 524 11 HOH HOH . G 5 HOH B 25 525 25 HOH HOH . G 5 HOH B 26 526 87 HOH HOH . G 5 HOH B 27 527 34 HOH HOH . G 5 HOH B 28 528 24 HOH HOH . G 5 HOH B 29 529 48 HOH HOH . G 5 HOH B 30 530 3 HOH HOH . G 5 HOH B 31 531 23 HOH HOH . G 5 HOH B 32 532 41 HOH HOH . G 5 HOH B 33 533 72 HOH HOH . G 5 HOH B 34 534 20 HOH HOH . G 5 HOH B 35 535 32 HOH HOH . G 5 HOH B 36 536 18 HOH HOH . G 5 HOH B 37 537 60 HOH HOH . G 5 HOH B 38 538 33 HOH HOH . G 5 HOH B 39 539 28 HOH HOH . G 5 HOH B 40 540 21 HOH HOH . G 5 HOH B 41 541 8 HOH HOH . G 5 HOH B 42 542 31 HOH HOH . G 5 HOH B 43 543 83 HOH HOH . G 5 HOH B 44 544 68 HOH HOH . G 5 HOH B 45 545 54 HOH HOH . G 5 HOH B 46 546 76 HOH HOH . G 5 HOH B 47 547 59 HOH HOH . G 5 HOH B 48 548 64 HOH HOH . G 5 HOH B 49 549 4 HOH HOH . G 5 HOH B 50 550 40 HOH HOH . G 5 HOH B 51 551 74 HOH HOH . G 5 HOH B 52 552 37 HOH HOH . G 5 HOH B 53 553 86 HOH HOH . G 5 HOH B 54 554 69 HOH HOH . G 5 HOH B 55 555 93 HOH HOH . G 5 HOH B 56 556 84 HOH HOH . G 5 HOH B 57 557 46 HOH HOH . G 5 HOH B 58 558 13 HOH HOH . G 5 HOH B 59 559 51 HOH HOH . G 5 HOH B 60 560 88 HOH HOH . G 5 HOH B 61 561 56 HOH HOH . G 5 HOH B 62 562 44 HOH HOH . G 5 HOH B 63 563 61 HOH HOH . G 5 HOH B 64 564 42 HOH HOH . G 5 HOH B 65 565 81 HOH HOH . G 5 HOH B 66 566 78 HOH HOH . G 5 HOH B 67 567 1 HOH HOH . G 5 HOH B 68 568 10 HOH HOH . G 5 HOH B 69 569 36 HOH HOH . G 5 HOH B 70 570 58 HOH HOH . G 5 HOH B 71 571 82 HOH HOH . G 5 HOH B 72 572 89 HOH HOH . G 5 HOH B 73 573 62 HOH HOH . G 5 HOH B 74 574 14 HOH HOH . G 5 HOH B 75 575 71 HOH HOH . G 5 HOH B 76 576 85 HOH HOH . G 5 HOH B 77 577 63 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 NAI . . . D 4 47.894 -20.378 34.368 1 133.77 ? PA NAI 402 A 1 HETATM 2 O O1A NAI . . . D 4 48.446 -19.268 35.231 1 136.02 ? O1A NAI 402 A 1 HETATM 3 O O2A NAI . . . D 4 46.909 -20.036 33.265 1 133.83 ? O2A NAI 402 A 1 HETATM 4 O O5B NAI . . . D 4 49.153 -21.165 33.721 1 137.41 ? O5B NAI 402 A 1 HETATM 5 C C5B NAI . . . D 4 50.071 -20.467 32.863 1 136.86 ? C5B NAI 402 A 1 HETATM 6 C C4B NAI . . . D 4 51.539 -20.509 33.324 1 137.16 ? C4B NAI 402 A 1 HETATM 7 O O4B NAI . . . D 4 52.163 -19.257 33 1 137.85 ? O4B NAI 402 A 1 HETATM 8 C C3B NAI . . . D 4 51.754 -20.746 34.818 1 137.78 ? C3B NAI 402 A 1 HETATM 9 O O3B NAI . . . D 4 52.615 -21.88 34.986 1 139.17 ? O3B NAI 402 A 1 HETATM 10 C C2B NAI . . . D 4 52.387 -19.473 35.369 1 137.69 ? C2B NAI 402 A 1 HETATM 11 O O2B NAI . . . D 4 53.601 -19.721 36.089 1 138.09 ? O2B NAI 402 A 1 HETATM 12 C C1B NAI . . . D 4 52.653 -18.572 34.165 1 137.45 ? C1B NAI 402 A 1 HETATM 13 N N9A NAI . . . D 4 51.924 -17.285 34.332 1 135.37 ? N9A NAI 402 A 1 HETATM 14 C C8A NAI . . . D 4 50.584 -17.127 34.223 1 134.32 ? C8A NAI 402 A 1 HETATM 15 N N7A NAI . . . D 4 50.218 -15.84 34.434 1 134.6 ? N7A NAI 402 A 1 HETATM 16 C C5A NAI . . . D 4 51.34 -15.136 34.679 1 133.06 ? C5A NAI 402 A 1 HETATM 17 C C6A NAI . . . D 4 51.665 -13.715 34.981 1 128.78 ? C6A NAI 402 A 1 HETATM 18 N N6A NAI . . . D 4 50.684 -12.782 35.057 1 124.73 ? N6A NAI 402 A 1 HETATM 19 N N1A NAI . . . D 4 52.974 -13.389 35.177 1 128.95 ? N1A NAI 402 A 1 HETATM 20 C C2A NAI . . . D 4 53.963 -14.313 35.102 1 132.87 ? C2A NAI 402 A 1 HETATM 21 N N3A NAI . . . D 4 53.736 -15.619 34.829 1 134.71 ? N3A NAI 402 A 1 HETATM 22 C C4A NAI . . . D 4 52.468 -16.091 34.613 1 134.22 ? C4A NAI 402 A 1 HETATM 23 O O3 NAI . . . D 4 47.244 -21.446 35.401 1 136.4 ? O3 NAI 402 A 1 HETATM 24 P PN NAI . . . D 4 46.367 -22.746 34.995 1 135.21 ? PN NAI 402 A 1 HETATM 25 O O1N NAI . . . D 4 47.168 -23.981 35.347 1 135.77 ? O1N NAI 402 A 1 HETATM 26 O O2N NAI . . . D 4 45.802 -22.601 33.601 1 134.56 ? O2N NAI 402 A 1 HETATM 27 O O5D NAI . . . D 4 45.126 -22.666 36.023 1 133.88 ? O5D NAI 402 A 1 HETATM 28 C C5D NAI . . . D 4 45.297 -22.574 37.44 1 128.89 ? C5D NAI 402 A 1 HETATM 29 C C4D NAI . . . D 4 44.064 -21.909 38.048 1 126.06 ? C4D NAI 402 A 1 HETATM 30 O O4D NAI . . . D 4 43.761 -20.698 37.344 1 124.89 ? O4D NAI 402 A 1 HETATM 31 C C3D NAI . . . D 4 42.833 -22.805 37.958 1 124.93 ? C3D NAI 402 A 1 HETATM 32 O O3D NAI . . . D 4 42.252 -22.961 39.26 1 121.8 ? O3D NAI 402 A 1 HETATM 33 C C2D NAI . . . D 4 41.885 -22.094 37.001 1 124.51 ? C2D NAI 402 A 1 HETATM 34 O O2D NAI . . . D 4 40.51 -22.156 37.398 1 125.71 ? O2D NAI 402 A 1 HETATM 35 C C1D NAI . . . D 4 42.37 -20.649 37.006 1 123.99 ? C1D NAI 402 A 1 HETATM 36 N N1N NAI . . . D 4 42.073 -19.935 35.748 1 121.04 ? N1N NAI 402 A 1 HETATM 37 C C2N NAI . . . D 4 41.276 -18.851 35.849 1 119.72 ? C2N NAI 402 A 1 HETATM 38 C C3N NAI . . . D 4 40.905 -18.08 34.742 1 117.8 ? C3N NAI 402 A 1 HETATM 39 C C7N NAI . . . D 4 40.008 -16.878 34.942 1 116.06 ? C7N NAI 402 A 1 HETATM 40 O O7N NAI . . . D 4 39.678 -16.549 36.076 1 111.79 ? O7N NAI 402 A 1 HETATM 41 N N7N NAI . . . D 4 39.586 -16.18 33.884 1 113.2 ? N7N NAI 402 A 1 HETATM 42 C C4N NAI . . . D 4 41.409 -18.458 33.354 1 116.54 ? C4N NAI 402 A 1 HETATM 43 C C5N NAI . . . D 4 42.268 -19.647 33.365 1 116.47 ? C5N NAI 402 A 1 HETATM 44 C C6N NAI . . . D 4 42.564 -20.332 34.55 1 117.87 ? C6N NAI 402 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 226 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 44 #