data_6VDJ # _model_server_result.job_id Jg7OM_Et-83B5IzP6KkQKA _model_server_result.datetime_utc '2025-02-05 04:50:59' _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 6vdj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6VDJ # _exptl.entry_id 6VDJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 667.457 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1,4,5,6-TETRAHYDRONICOTINAMIDE 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 6VDJ _cell.length_a 84.695 _cell.length_b 84.695 _cell.length_c 196.007 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VDJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _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,D,E,F,G _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' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -130.671333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C21 H31 N7 O14 P2' _chem_comp.formula_weight 667.457 _chem_comp.id TXD _chem_comp.mon_nstd_flag n _chem_comp.name '1,4,5,6-TETRAHYDRONICOTINAMIDE 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 O7N C7N TXD doub 338 n n C7N C3N TXD sing 339 n n C7N N7N TXD sing 340 n n N7N H7N1 TXD sing 341 n n N7N H7N2 TXD sing 342 n n C3N C4N TXD sing 343 n n C3N C2N TXD sing 344 n n C3N H3N TXD sing 345 n n C2N N1N TXD sing 346 n n C2N H2N1 TXD sing 347 n n C2N H2N2 TXD sing 348 n n C4N C5N TXD doub 349 n n C4N H4N TXD sing 350 n n C5N C6N TXD sing 351 n n C5N H5N TXD sing 352 n n C6N N1N TXD sing 353 n n C6N H6N1 TXD sing 354 n n C6N H6N2 TXD sing 355 n n N1N "C1'A" TXD sing 356 n n "C1'A" "O4'A" TXD sing 357 n n "C1'A" "C2'A" TXD sing 358 n n "C1'A" "H1'A" TXD sing 359 n n "O4'A" "C4'A" TXD sing 360 n n "C2'A" "C3'A" TXD sing 361 n n "C2'A" "O2'A" TXD sing 362 n n "C2'A" "H2'A" TXD sing 363 n n "O2'A" HO2A TXD sing 364 n n "C3'A" "C4'A" TXD sing 365 n n "C3'A" "O3'A" TXD sing 366 n n "C3'A" "H3'A" TXD sing 367 n n "O3'A" HO3A TXD sing 368 n n "C4'A" "C5'A" TXD sing 369 n n "C4'A" "H4'A" TXD sing 370 n n "C5'A" "O5'A" TXD sing 371 n n "C5'A" "H5'1" TXD sing 372 n n "C5'A" "H5'2" TXD sing 373 n n "O5'A" PN TXD sing 374 n n PN O1N TXD doub 375 n n PN O2N TXD sing 376 n n PN O3 TXD sing 377 n n O2N HO2N TXD sing 378 n n O3 PA TXD sing 379 n n PA O1P TXD doub 380 n n PA O5' TXD sing 381 n n PA O2P TXD sing 382 n n O2P HO2P TXD sing 383 n n O5' C5' TXD sing 384 n n C5' C4' TXD sing 385 n n C5' "H5'A" TXD sing 386 n n C5' "H5'B" TXD sing 387 n n C4' O4' TXD sing 388 n n C4' C3' TXD sing 389 n n C4' H4' TXD sing 390 n n C3' O3' TXD sing 391 n n C3' C2' TXD sing 392 n n C3' H3' TXD sing 393 n n O3' HO3' TXD sing 394 n n C2' C1' TXD sing 395 n n C2' O2' TXD sing 396 n n C2' H2' TXD sing 397 n n O2' HO2' TXD sing 398 n n C1' O4' TXD sing 399 n n C1' N9A TXD sing 400 n n C1' H1' TXD sing 401 n n N9A C4A TXD sing 402 n y N9A C8A TXD sing 403 n y C4A N3A TXD sing 404 n y C4A C5A TXD doub 405 n y N3A C2A TXD doub 406 n y C2A N1A TXD sing 407 n y C2A H2A TXD sing 408 n n N1A C6A TXD doub 409 n y C6A C5A TXD sing 410 n y C6A N6A TXD sing 411 n n N6A H6A1 TXD sing 412 n n N6A H6A2 TXD sing 413 n n C5A N7A TXD sing 414 n y N7A C8A TXD doub 415 n y C8A H8A TXD sing 416 n n # _atom_sites.entry_id 6VDJ _atom_sites.fract_transf_matrix[1][1] 0.011807 _atom_sites.fract_transf_matrix[1][2] 0.006817 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013634 _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] 0.005102 _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 2 TXD A 1 401 401 TXD TXD . D 3 SO4 A 1 402 1 SO4 SO4 . E 3 SO4 B 1 401 2 SO4 SO4 . F 4 HOH A 1 501 15 HOH HOH . F 4 HOH A 2 502 7 HOH HOH . F 4 HOH A 3 503 1 HOH HOH . F 4 HOH A 4 504 4 HOH HOH . F 4 HOH A 5 505 3 HOH HOH . F 4 HOH A 6 506 9 HOH HOH . F 4 HOH A 7 507 14 HOH HOH . F 4 HOH A 8 508 12 HOH HOH . F 4 HOH A 9 509 10 HOH HOH . G 4 HOH B 1 501 2 HOH HOH . G 4 HOH B 2 502 6 HOH HOH . G 4 HOH B 3 503 13 HOH HOH . G 4 HOH B 4 504 5 HOH HOH . G 4 HOH B 5 505 8 HOH HOH . G 4 HOH B 6 506 11 HOH HOH . G 4 HOH B 7 507 16 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 O7N TXD . . . C 2 -20.645 33.52 -40.124 1 90.2 ? O7N TXD 401 A 1 HETATM 2 C C7N TXD . . . C 2 -20.248 34.616 -40.151 1 82.01 ? C7N TXD 401 A 1 HETATM 3 N N7N TXD . . . C 2 -21.199 35.734 -39.854 1 77.38 ? N7N TXD 401 A 1 HETATM 4 C C3N TXD . . . C 2 -18.768 34.892 -40.425 1 92.09 ? C3N TXD 401 A 1 HETATM 5 C C2N TXD . . . C 2 -18.413 36.306 -39.534 1 102.17 ? C2N TXD 401 A 1 HETATM 6 C C4N TXD . . . C 2 -18.034 33.784 -40.037 1 84.14 ? C4N TXD 401 A 1 HETATM 7 C C5N TXD . . . C 2 -16.529 34.043 -39.708 1 83.64 ? C5N TXD 401 A 1 HETATM 8 C C6N TXD . . . C 2 -16.197 35.33 -39.061 1 88.85 ? C6N TXD 401 A 1 HETATM 9 N N1N TXD . . . C 2 -17.15 36.617 -39.456 1 90.2 ? N1N TXD 401 A 1 HETATM 10 C "C1'A" TXD . . . C 2 -17.061 37.843 -38.569 1 96.17 ? "C1'A" TXD 401 A 1 HETATM 11 O "O4'A" TXD . . . C 2 -16.504 39.149 -39.393 1 86 ? "O4'A" TXD 401 A 1 HETATM 12 C "C2'A" TXD . . . C 2 -16.288 37.839 -37.517 1 95.74 ? "C2'A" TXD 401 A 1 HETATM 13 O "O2'A" TXD . . . C 2 -17.133 37.885 -36.313 1 89.97 ? "O2'A" TXD 401 A 1 HETATM 14 C "C3'A" TXD . . . C 2 -15.444 39.171 -37.569 1 96.57 ? "C3'A" TXD 401 A 1 HETATM 15 O "O3'A" TXD . . . C 2 -16.087 40.29 -37.125 1 90.68 ? "O3'A" TXD 401 A 1 HETATM 16 C "C4'A" TXD . . . C 2 -15.218 39.306 -39.058 1 89.7 ? "C4'A" TXD 401 A 1 HETATM 17 C "C5'A" TXD . . . C 2 -14.379 38.201 -39.652 1 87.78 ? "C5'A" TXD 401 A 1 HETATM 18 O "O5'A" TXD . . . C 2 -13.672 38.648 -40.839 1 85.54 ? "O5'A" TXD 401 A 1 HETATM 19 P PN TXD . . . C 2 -11.996 38.479 -40.82 1 92.98 ? PN TXD 401 A 1 HETATM 20 O O1N TXD . . . C 2 -11.345 38.994 -42.096 1 78.4 ? O1N TXD 401 A 1 HETATM 21 O O2N TXD . . . C 2 -11.608 37.028 -40.651 1 82.88 ? O2N TXD 401 A 1 HETATM 22 O O3 TXD . . . C 2 -11.409 39.324 -39.458 1 97.59 ? O3 TXD 401 A 1 HETATM 23 P PA TXD . . . C 2 -10.042 40.331 -39.648 1 98.09 ? PA TXD 401 A 1 HETATM 24 O O2P TXD . . . C 2 -9.385 40.667 -38.317 1 98.72 ? O2P TXD 401 A 1 HETATM 25 O O1P TXD . . . C 2 -9.031 39.62 -40.531 1 105.03 ? O1P TXD 401 A 1 HETATM 26 O O5' TXD . . . C 2 -10.549 41.756 -40.393 1 90.27 ? O5' TXD 401 A 1 HETATM 27 C C5' TXD . . . C 2 -11.372 42.71 -39.677 1 90.48 ? C5' TXD 401 A 1 HETATM 28 C C4' TXD . . . C 2 -11.167 43.996 -40.433 1 87.33 ? C4' TXD 401 A 1 HETATM 29 C C3' TXD . . . C 2 -9.807 44.813 -39.888 1 95.58 ? C3' TXD 401 A 1 HETATM 30 O O3' TXD . . . C 2 -8.799 44.621 -40.934 1 86.97 ? O3' TXD 401 A 1 HETATM 31 C C2' TXD . . . C 2 -10.1 46.036 -39.719 1 90.1 ? C2' TXD 401 A 1 HETATM 32 O O2' TXD . . . C 2 -8.953 46.927 -40.14 1 95.69 ? O2' TXD 401 A 1 HETATM 33 C C1' TXD . . . C 2 -11.409 46.162 -40.578 1 88.5 ? C1' TXD 401 A 1 HETATM 34 O O4' TXD . . . C 2 -12.093 44.833 -40.203 1 93.79 ? O4' TXD 401 A 1 HETATM 35 N N9A TXD . . . C 2 -12.094 47.224 -40.274 1 87.24 ? N9A TXD 401 A 1 HETATM 36 C C4A TXD . . . C 2 -12.421 47.908 -39.181 1 87.69 ? C4A TXD 401 A 1 HETATM 37 N N3A TXD . . . C 2 -12.167 47.739 -37.877 1 87.81 ? N3A TXD 401 A 1 HETATM 38 C C2A TXD . . . C 2 -12.671 48.621 -37.014 1 90.45 ? C2A TXD 401 A 1 HETATM 39 N N1A TXD . . . C 2 -13.442 49.697 -37.413 1 87.89 ? N1A TXD 401 A 1 HETATM 40 C C6A TXD . . . C 2 -13.673 49.844 -38.678 1 86.41 ? C6A TXD 401 A 1 HETATM 41 N N6A TXD . . . C 2 -14.418 50.859 -39.419 1 85.49 ? N6A TXD 401 A 1 HETATM 42 C C5A TXD . . . C 2 -13.165 48.951 -39.576 1 89.37 ? C5A TXD 401 A 1 HETATM 43 N N7A TXD . . . C 2 -13.281 48.914 -40.886 1 86.13 ? N7A TXD 401 A 1 HETATM 44 C C8A TXD . . . C 2 -12.612 47.845 -41.32 1 85.93 ? C8A TXD 401 A 1 HETATM 45 H H7N1 TXD . . . C 2 -20.899 36.533 -39.866 1 92.9 ? H7N1 TXD 401 A 1 HETATM 46 H H7N2 TXD . . . C 2 -22.034 35.589 -39.681 1 92.9 ? H7N2 TXD 401 A 1 HETATM 47 H H2N1 TXD . . . C 2 -18.88 37.049 -39.948 1 122.64 ? H2N1 TXD 401 A 1 HETATM 48 H H2N2 TXD . . . C 2 -18.748 36.185 -38.632 1 122.64 ? H2N2 TXD 401 A 1 HETATM 49 H H6N1 TXD . . . C 2 -15.284 35.552 -39.298 1 106.65 ? H6N1 TXD 401 A 1 HETATM 50 H H6N2 TXD . . . C 2 -16.255 35.201 -38.101 1 106.65 ? H6N2 TXD 401 A 1 HETATM 51 H H3N TXD . . . C 2 -18.586 35.032 -41.368 1 110.54 ? H3N TXD 401 A 1 HETATM 52 H H4N TXD . . . C 2 -18.414 32.938 -39.976 1 101.01 ? H4N TXD 401 A 1 HETATM 53 H H5N TXD . . . C 2 -15.872 33.416 -39.91 1 100.41 ? H5N TXD 401 A 1 HETATM 54 H "H1'A" TXD . . . C 2 -17.971 37.912 -38.242 1 115.44 ? "H1'A" TXD 401 A 1 HETATM 55 H "H2'A" TXD . . . C 2 -15.704 37.065 -37.543 1 114.92 ? "H2'A" TXD 401 A 1 HETATM 56 H HO2A TXD . . . C 2 -17.703 38.508 -36.458 1 108 ? HO2A TXD 401 A 1 HETATM 57 H "H3'A" TXD . . . C 2 -14.646 39.067 -37.026 1 115.91 ? "H3'A" TXD 401 A 1 HETATM 58 H HO3A TXD . . . C 2 -15.767 40.959 -37.566 1 108.85 ? HO3A TXD 401 A 1 HETATM 59 H "H4'A" TXD . . . C 2 -14.78 40.129 -39.325 1 107.67 ? "H4'A" TXD 401 A 1 HETATM 60 H "H5'1" TXD . . . C 2 -14.959 37.46 -39.889 1 105.38 ? "H5'1" TXD 401 A 1 HETATM 61 H "H5'2" TXD . . . C 2 -13.734 37.906 -38.991 1 105.38 ? "H5'2" TXD 401 A 1 HETATM 62 H "H5'A" TXD . . . C 2 -11.079 42.799 -38.757 1 108.61 ? "H5'A" TXD 401 A 1 HETATM 63 H "H5'B" TXD . . . C 2 -12.305 42.444 -39.694 1 108.61 ? "H5'B" TXD 401 A 1 HETATM 64 H H4' TXD . . . C 2 -11.109 43.778 -41.376 1 104.84 ? H4' TXD 401 A 1 HETATM 65 H H3' TXD . . . C 2 -9.518 44.5 -39.016 1 114.74 ? H3' TXD 401 A 1 HETATM 66 H HO3' TXD . . . C 2 -8.888 43.885 -41.362 1 104.4 ? HO3' TXD 401 A 1 HETATM 67 H H2' TXD . . . C 2 -10.289 46.279 -38.799 1 108.16 ? H2' TXD 401 A 1 HETATM 68 H HO2' TXD . . . C 2 -8.886 47.596 -39.608 1 114.87 ? HO2' TXD 401 A 1 HETATM 69 H H1' TXD . . . C 2 -11.253 46.229 -41.533 1 106.24 ? H1' TXD 401 A 1 HETATM 70 H H2A TXD . . . C 2 -12.554 48.594 -36.092 1 108.57 ? H2A TXD 401 A 1 HETATM 71 H H6A1 TXD . . . C 2 -14.435 51.668 -39.134 1 102.62 ? H6A1 TXD 401 A 1 HETATM 72 H H6A2 TXD . . . C 2 -14.805 50.642 -40.151 1 102.62 ? H6A2 TXD 401 A 1 HETATM 73 H H8A TXD . . . C 2 -12.525 47.581 -42.207 1 103.15 ? H8A TXD 401 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 368 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 73 #