data_1D8A # _model_server_result.job_id ri7aM-9zHHbN_tiVg3JRZA _model_server_result.datetime_utc '2025-03-04 21:19:25' _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 1d8a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 1D8A # _exptl.entry_id 1D8A _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 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 1D8A _cell.length_a 80.6 _cell.length_b 80.6 _cell.length_c 327.6 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D8A _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,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,D,E,F,G,H _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' 10_666 -y+1,-x+1,-z+11/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 40.3 69.801648 600.6 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 1D8A _atom_sites.fract_transf_matrix[1][1] 0.012407 _atom_sites.fract_transf_matrix[1][2] 0.007163 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014326 _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] 0.003053 _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 NAD A 1 501 501 NAD NAD . D 3 TCL A 1 502 502 TCL TCL . E 2 NAD B 1 503 501 NAD NAD . F 3 TCL B 1 504 502 TCL TCL . G 4 HOH A 1 503 2 HOH WAT . G 4 HOH A 2 504 3 HOH WAT . G 4 HOH A 3 505 4 HOH WAT . G 4 HOH A 4 506 9 HOH WAT . G 4 HOH A 5 507 10 HOH WAT . G 4 HOH A 6 508 14 HOH WAT . G 4 HOH A 7 509 16 HOH WAT . G 4 HOH A 8 510 18 HOH WAT . G 4 HOH A 9 511 20 HOH WAT . G 4 HOH A 10 512 21 HOH WAT . G 4 HOH A 11 513 24 HOH WAT . G 4 HOH A 12 514 25 HOH WAT . G 4 HOH A 13 515 26 HOH WAT . G 4 HOH A 14 516 28 HOH WAT . G 4 HOH A 15 517 29 HOH WAT . G 4 HOH A 16 518 35 HOH WAT . G 4 HOH A 17 519 36 HOH WAT . G 4 HOH A 18 520 38 HOH WAT . G 4 HOH A 19 521 39 HOH WAT . G 4 HOH A 20 522 40 HOH WAT . G 4 HOH A 21 523 41 HOH WAT . G 4 HOH A 22 524 43 HOH WAT . G 4 HOH A 23 525 44 HOH WAT . G 4 HOH A 24 526 48 HOH WAT . G 4 HOH A 25 527 49 HOH WAT . G 4 HOH A 26 528 50 HOH WAT . G 4 HOH A 27 529 51 HOH WAT . G 4 HOH A 28 530 54 HOH WAT . G 4 HOH A 29 531 57 HOH WAT . G 4 HOH A 30 532 58 HOH WAT . G 4 HOH A 31 533 59 HOH WAT . G 4 HOH A 32 534 63 HOH WAT . G 4 HOH A 33 535 65 HOH WAT . G 4 HOH A 34 536 66 HOH WAT . G 4 HOH A 35 537 68 HOH WAT . G 4 HOH A 36 538 69 HOH WAT . G 4 HOH A 37 539 72 HOH WAT . G 4 HOH A 38 540 73 HOH WAT . G 4 HOH A 39 541 76 HOH WAT . G 4 HOH A 40 542 79 HOH WAT . G 4 HOH A 41 543 83 HOH WAT . G 4 HOH A 42 544 86 HOH WAT . G 4 HOH A 43 545 87 HOH WAT . G 4 HOH A 44 546 89 HOH WAT . G 4 HOH A 45 547 96 HOH WAT . G 4 HOH A 46 548 98 HOH WAT . G 4 HOH A 47 549 99 HOH WAT . G 4 HOH A 48 550 103 HOH WAT . G 4 HOH A 49 551 104 HOH WAT . G 4 HOH A 50 552 105 HOH WAT . G 4 HOH A 51 553 106 HOH WAT . G 4 HOH A 52 554 107 HOH WAT . G 4 HOH A 53 555 109 HOH WAT . G 4 HOH A 54 556 114 HOH WAT . G 4 HOH A 55 557 116 HOH WAT . G 4 HOH A 56 558 117 HOH WAT . G 4 HOH A 57 559 118 HOH WAT . G 4 HOH A 58 560 119 HOH WAT . H 4 HOH B 1 505 1 HOH WAT . H 4 HOH B 2 506 5 HOH WAT . H 4 HOH B 3 507 6 HOH WAT . H 4 HOH B 4 508 7 HOH WAT . H 4 HOH B 5 509 8 HOH WAT . H 4 HOH B 6 510 11 HOH WAT . H 4 HOH B 7 511 12 HOH WAT . H 4 HOH B 8 512 13 HOH WAT . H 4 HOH B 9 513 15 HOH WAT . H 4 HOH B 10 514 17 HOH WAT . H 4 HOH B 11 515 19 HOH WAT . H 4 HOH B 12 516 22 HOH WAT . H 4 HOH B 13 517 23 HOH WAT . H 4 HOH B 14 518 27 HOH WAT . H 4 HOH B 15 519 30 HOH WAT . H 4 HOH B 16 520 31 HOH WAT . H 4 HOH B 17 521 32 HOH WAT . H 4 HOH B 18 522 33 HOH WAT . H 4 HOH B 19 523 34 HOH WAT . H 4 HOH B 20 524 37 HOH WAT . H 4 HOH B 21 525 42 HOH WAT . H 4 HOH B 22 526 45 HOH WAT . H 4 HOH B 23 527 46 HOH WAT . H 4 HOH B 24 528 47 HOH WAT . H 4 HOH B 25 529 52 HOH WAT . H 4 HOH B 26 530 53 HOH WAT . H 4 HOH B 27 531 55 HOH WAT . H 4 HOH B 28 532 56 HOH WAT . H 4 HOH B 29 533 60 HOH WAT . H 4 HOH B 30 534 61 HOH WAT . H 4 HOH B 31 535 62 HOH WAT . H 4 HOH B 32 536 64 HOH WAT . H 4 HOH B 33 537 67 HOH WAT . H 4 HOH B 34 538 70 HOH WAT . H 4 HOH B 35 539 71 HOH WAT . H 4 HOH B 36 540 74 HOH WAT . H 4 HOH B 37 541 75 HOH WAT . H 4 HOH B 38 542 77 HOH WAT . H 4 HOH B 39 543 78 HOH WAT . H 4 HOH B 40 544 80 HOH WAT . H 4 HOH B 41 545 81 HOH WAT . H 4 HOH B 42 546 82 HOH WAT . H 4 HOH B 43 547 84 HOH WAT . H 4 HOH B 44 548 85 HOH WAT . H 4 HOH B 45 549 88 HOH WAT . H 4 HOH B 46 550 90 HOH WAT . H 4 HOH B 47 551 91 HOH WAT . H 4 HOH B 48 552 92 HOH WAT . H 4 HOH B 49 553 93 HOH WAT . H 4 HOH B 50 554 94 HOH WAT . H 4 HOH B 51 555 95 HOH WAT . H 4 HOH B 52 556 97 HOH WAT . H 4 HOH B 53 557 100 HOH WAT . H 4 HOH B 54 558 101 HOH WAT . H 4 HOH B 55 559 102 HOH WAT . H 4 HOH B 56 560 108 HOH WAT . H 4 HOH B 57 561 110 HOH WAT . H 4 HOH B 58 562 111 HOH WAT . H 4 HOH B 59 563 112 HOH WAT . H 4 HOH B 60 564 113 HOH WAT . H 4 HOH B 61 565 115 HOH WAT . # 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 . . . C 2 6.658 16.508 300.573 1 16.98 ? PA NAD 501 A 1 HETATM 2 O O1A NAD . . . C 2 5.404 15.652 300.603 1 47.15 ? O1A NAD 501 A 1 HETATM 3 O O2A NAD . . . C 2 7.913 16.022 299.886 1 38.5 ? O2A NAD 501 A 1 HETATM 4 O O5B NAD . . . C 2 7.025 16.948 302.05 1 35.28 ? O5B NAD 501 A 1 HETATM 5 C C5B NAD . . . C 2 5.99 17.219 303.086 1 13.2 ? C5B NAD 501 A 1 HETATM 6 C C4B NAD . . . C 2 6.39 16.552 304.325 1 36.83 ? C4B NAD 501 A 1 HETATM 7 O O4B NAD . . . C 2 5.483 16.894 305.447 1 27.98 ? O4B NAD 501 A 1 HETATM 8 C C3B NAD . . . C 2 6.423 14.976 304.366 1 22.11 ? C3B NAD 501 A 1 HETATM 9 O O3B NAD . . . C 2 7.846 14.544 304.436 1 30.8 ? O3B NAD 501 A 1 HETATM 10 C C2B NAD . . . C 2 5.638 14.537 305.589 1 40.82 ? C2B NAD 501 A 1 HETATM 11 O O2B NAD . . . C 2 6.085 13.48 306.28 1 62.8 ? O2B NAD 501 A 1 HETATM 12 C C1B NAD . . . C 2 5.639 15.877 306.365 1 47.83 ? C1B NAD 501 A 1 HETATM 13 N N9A NAD . . . C 2 4.517 15.943 307.254 1 44.72 ? N9A NAD 501 A 1 HETATM 14 C C8A NAD . . . C 2 3.187 16.155 306.998 1 13.95 ? C8A NAD 501 A 1 HETATM 15 N N7A NAD . . . C 2 2.396 16.13 308.046 1 37.17 ? N7A NAD 501 A 1 HETATM 16 C C5A NAD . . . C 2 3.182 15.882 309.095 1 38.36 ? C5A NAD 501 A 1 HETATM 17 C C6A NAD . . . C 2 2.85 15.744 310.523 1 16.72 ? C6A NAD 501 A 1 HETATM 18 N N6A NAD . . . C 2 1.656 15.845 311.053 1 46.57 ? N6A NAD 501 A 1 HETATM 19 N N1A NAD . . . C 2 3.961 15.488 311.284 1 25.69 ? N1A NAD 501 A 1 HETATM 20 C C2A NAD . . . C 2 5.213 15.367 310.853 1 19.86 ? C2A NAD 501 A 1 HETATM 21 N N3A NAD . . . C 2 5.57 15.49 309.514 1 25.29 ? N3A NAD 501 A 1 HETATM 22 C C4A NAD . . . C 2 4.517 15.751 308.645 1 26.72 ? C4A NAD 501 A 1 HETATM 23 O O3 NAD . . . C 2 6.33 17.915 299.985 1 61.92 ? O3 NAD 501 A 1 HETATM 24 P PN NAD . . . C 2 7.251 19.271 299.715 1 17.95 ? PN NAD 501 A 1 HETATM 25 O O1N NAD . . . C 2 6.774 19.872 298.485 1 24.16 ? O1N NAD 501 A 1 HETATM 26 O O2N NAD . . . C 2 8.677 18.937 299.925 1 46.54 ? O2N NAD 501 A 1 HETATM 27 O O5D NAD . . . C 2 6.853 20.193 300.963 1 20.7 ? O5D NAD 501 A 1 HETATM 28 C C5D NAD . . . C 2 7.854 20.989 301.672 1 22.49 ? C5D NAD 501 A 1 HETATM 29 C C4D NAD . . . C 2 7.288 22.226 302.216 1 50.31 ? C4D NAD 501 A 1 HETATM 30 O O4D NAD . . . C 2 7.459 23.281 301.115 1 23.8 ? O4D NAD 501 A 1 HETATM 31 C C3D NAD . . . C 2 5.726 22.332 302.472 1 28.65 ? C3D NAD 501 A 1 HETATM 32 O O3D NAD . . . C 2 5.608 23.242 303.503 1 22.9 ? O3D NAD 501 A 1 HETATM 33 C C2D NAD . . . C 2 5.12 22.822 301.122 1 21.95 ? C2D NAD 501 A 1 HETATM 34 O O2D NAD . . . C 2 3.896 23.418 301.275 1 21.7 ? O2D NAD 501 A 1 HETATM 35 C C1D NAD . . . C 2 6.209 23.833 300.755 1 22.15 ? C1D NAD 501 A 1 HETATM 36 N N1N NAD . . . C 2 6.255 24.271 299.276 1 22.81 ? N1N NAD 501 A 1 HETATM 37 C C2N NAD . . . C 2 6.178 23.329 298.264 1 17.72 ? C2N NAD 501 A 1 HETATM 38 C C3N NAD . . . C 2 6.228 23.88 297.017 1 48.33 ? C3N NAD 501 A 1 HETATM 39 C C7N NAD . . . C 2 6.153 22.74 295.936 1 14 ? C7N NAD 501 A 1 HETATM 40 O O7N NAD . . . C 2 6.165 23.071 294.763 1 40.49 ? O7N NAD 501 A 1 HETATM 41 N N7N NAD . . . C 2 6.04 21.473 296.385 1 30.19 ? N7N NAD 501 A 1 HETATM 42 C C4N NAD . . . C 2 6.333 25.234 296.673 1 51.64 ? C4N NAD 501 A 1 HETATM 43 C C5N NAD . . . C 2 6.395 26.086 297.808 1 14.05 ? C5N NAD 501 A 1 HETATM 44 C C6N NAD . . . C 2 6.355 25.606 299.09 1 17.4 ? C6N NAD 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #