data_1WDM # _model_server_result.job_id uWYBwfa-92GDa-bZEIMQGA _model_server_result.datetime_utc '2025-06-27 01:23:51' _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 1wdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1001}' # _entry.id 1WDM # _exptl.entry_id 1WDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 5 _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 111.79 _cell.angle_gamma 90 _cell.entry_id 1WDM _cell.length_a 181.453 _cell.length_b 95.462 _cell.length_c 161.325 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1WDM _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 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,H,I,J _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 ? 5 G N N ? 5 H 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 NE2 HIS 550 A HIS 550 1_555 E ZN ZN . A ZN 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc2 E ZN ZN . A ZN 716 1_555 D OE2 GLU 265 D GLU 266 3_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? # _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 326 n n PA O2A NAD sing 327 n n PA O5B NAD sing 328 n n PA O3 NAD sing 329 n n O2A HOA2 NAD sing 330 n n O5B C5B NAD sing 331 n n C5B C4B NAD sing 332 n n C5B H51A NAD sing 333 n n C5B H52A NAD sing 334 n n C4B O4B NAD sing 335 n n C4B C3B NAD sing 336 n n C4B H4B NAD sing 337 n n O4B C1B NAD sing 338 n n C3B O3B NAD sing 339 n n C3B C2B NAD sing 340 n n C3B H3B NAD sing 341 n n O3B HO3A NAD sing 342 n n C2B O2B NAD sing 343 n n C2B C1B NAD sing 344 n n C2B H2B NAD sing 345 n n O2B HO2A NAD sing 346 n n C1B N9A NAD sing 347 n n C1B H1B NAD sing 348 n n N9A C8A NAD sing 349 n y N9A C4A NAD sing 350 n y C8A N7A NAD doub 351 n y C8A H8A NAD sing 352 n n N7A C5A NAD sing 353 n y C5A C6A NAD sing 354 n y C5A C4A NAD doub 355 n y C6A N6A NAD sing 356 n n C6A N1A NAD doub 357 n y N6A H61A NAD sing 358 n n N6A H62A NAD sing 359 n n N1A C2A NAD sing 360 n y C2A N3A NAD doub 361 n y C2A H2A NAD sing 362 n n N3A C4A NAD sing 363 n y O3 PN NAD sing 364 n n PN O1N NAD doub 365 n n PN O2N NAD sing 366 n n PN O5D NAD sing 367 n n O5D C5D NAD sing 368 n n C5D C4D NAD sing 369 n n C5D H51N NAD sing 370 n n C5D H52N NAD sing 371 n n C4D O4D NAD sing 372 n n C4D C3D NAD sing 373 n n C4D H4D NAD sing 374 n n O4D C1D NAD sing 375 n n C3D O3D NAD sing 376 n n C3D C2D NAD sing 377 n n C3D H3D NAD sing 378 n n O3D HO3N NAD sing 379 n n C2D O2D NAD sing 380 n n C2D C1D NAD sing 381 n n C2D H2D NAD sing 382 n n O2D HO2N NAD sing 383 n n C1D N1N NAD sing 384 n n C1D H1D NAD sing 385 n n N1N C2N NAD sing 386 n y N1N C6N NAD doub 387 n y C2N C3N NAD doub 388 n y C2N H2N NAD sing 389 n n C3N C7N NAD sing 390 n n C3N C4N NAD sing 391 n y C7N O7N NAD doub 392 n n C7N N7N NAD sing 393 n n N7N H71N NAD sing 394 n n N7N H72N NAD sing 395 n n C4N C5N NAD doub 396 n y C4N H4N NAD sing 397 n n C5N C6N NAD sing 398 n y C5N H5N NAD sing 399 n n C6N H6N NAD sing 400 n n # _atom_sites.entry_id 1WDM _atom_sites.fract_transf_matrix[1][1] 0.005511 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002203 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010475 _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] 0.006676 _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 E 3 ZN A 1 716 1 ZN ZN2 . F 4 ACO A 1 1002 1002 ACO ACC . G 5 NAD A 1 1001 1001 NAD NAD . H 5 NAD B 1 2001 1001 NAD NAD . I 4 ACO C 1 3001 1001 ACO ACC . J 4 ACO D 1 4001 1001 ACO ACC . # 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 . . . G 5 -35.918 18.683 112.51 1 98.95 ? PA NAD 1001 A 1 HETATM 2 O O1A NAD . . . G 5 -34.659 18.658 111.71 1 98.95 ? O1A NAD 1001 A 1 HETATM 3 O O2A NAD . . . G 5 -36.832 17.523 112.323 1 98.95 ? O2A NAD 1001 A 1 HETATM 4 O O5B NAD . . . G 5 -35.539 18.734 114.063 1 98.95 ? O5B NAD 1001 A 1 HETATM 5 C C5B NAD . . . G 5 -36.554 18.81 115.077 1 98.95 ? C5B NAD 1001 A 1 HETATM 6 C C4B NAD . . . G 5 -35.96 19.274 116.4 1 98.95 ? C4B NAD 1001 A 1 HETATM 7 O O4B NAD . . . G 5 -37.042 19.716 117.291 1 98.95 ? O4B NAD 1001 A 1 HETATM 8 C C3B NAD . . . G 5 -35.256 18.156 117.174 1 98.95 ? C3B NAD 1001 A 1 HETATM 9 O O3B NAD . . . G 5 -34.093 18.646 117.846 1 98.95 ? O3B NAD 1001 A 1 HETATM 10 C C2B NAD . . . G 5 -36.322 17.69 118.171 1 98.95 ? C2B NAD 1001 A 1 HETATM 11 O O2B NAD . . . G 5 -35.793 17.054 119.315 1 98.95 ? O2B NAD 1001 A 1 HETATM 12 C C1B NAD . . . G 5 -36.94 19.031 118.529 1 98.95 ? C1B NAD 1001 A 1 HETATM 13 N N9A NAD . . . G 5 -38.282 18.904 119.129 1 98.95 ? N9A NAD 1001 A 1 HETATM 14 C C8A NAD . . . G 5 -39.356 18.147 118.696 1 98.95 ? C8A NAD 1001 A 1 HETATM 15 N N7A NAD . . . G 5 -40.422 18.246 119.456 1 98.95 ? N7A NAD 1001 A 1 HETATM 16 C C5A NAD . . . G 5 -40.039 19.128 120.457 1 98.95 ? C5A NAD 1001 A 1 HETATM 17 C C6A NAD . . . G 5 -40.713 19.658 121.601 1 98.95 ? C6A NAD 1001 A 1 HETATM 18 N N6A NAD . . . G 5 -41.978 19.359 121.912 1 98.95 ? N6A NAD 1001 A 1 HETATM 19 N N1A NAD . . . G 5 -40.031 20.53 122.417 1 98.95 ? N1A NAD 1001 A 1 HETATM 20 C C2A NAD . . . G 5 -38.747 20.843 122.115 1 98.95 ? C2A NAD 1001 A 1 HETATM 21 N N3A NAD . . . G 5 -38.006 20.408 121.072 1 98.95 ? N3A NAD 1001 A 1 HETATM 22 C C4A NAD . . . G 5 -38.715 19.537 120.276 1 98.95 ? C4A NAD 1001 A 1 HETATM 23 O O3 NAD . . . G 5 -36.728 20.007 112.114 1 98.95 ? O3 NAD 1001 A 1 HETATM 24 P PN NAD . . . G 5 -36.009 21.442 112.056 1 98.95 ? PN NAD 1001 A 1 HETATM 25 O O1N NAD . . . G 5 -34.986 21.515 113.143 1 98.95 ? O1N NAD 1001 A 1 HETATM 26 O O2N NAD . . . G 5 -35.503 21.616 110.667 1 98.95 ? O2N NAD 1001 A 1 HETATM 27 O O5D NAD . . . G 5 -37.087 22.58 112.324 1 98.95 ? O5D NAD 1001 A 1 HETATM 28 C C5D NAD . . . G 5 -38.368 22.532 111.701 1 98.95 ? C5D NAD 1001 A 1 HETATM 29 C C4D NAD . . . G 5 -38.955 23.924 111.591 1 98.95 ? C4D NAD 1001 A 1 HETATM 30 O O4D NAD . . . G 5 -38.122 24.716 110.686 1 98.95 ? O4D NAD 1001 A 1 HETATM 31 C C3D NAD . . . G 5 -40.349 23.923 110.97 1 98.95 ? C3D NAD 1001 A 1 HETATM 32 O O3D NAD . . . G 5 -41.183 24.903 111.592 1 98.95 ? O3D NAD 1001 A 1 HETATM 33 C C2D NAD . . . G 5 -40.078 24.255 109.492 1 98.95 ? C2D NAD 1001 A 1 HETATM 34 O O2D NAD . . . G 5 -41.175 24.857 108.838 1 98.95 ? O2D NAD 1001 A 1 HETATM 35 C C1D NAD . . . G 5 -38.909 25.228 109.619 1 98.95 ? C1D NAD 1001 A 1 HETATM 36 N N1N NAD . . . G 5 -38.162 25.37 108.347 1 98.95 ? N1N NAD 1001 A 1 HETATM 37 C C2N NAD . . . G 5 -37.494 24.268 107.808 1 98.95 ? C2N NAD 1001 A 1 HETATM 38 C C3N NAD . . . G 5 -36.789 24.385 106.617 1 98.95 ? C3N NAD 1001 A 1 HETATM 39 C C7N NAD . . . G 5 -36.032 23.145 105.991 1 98.95 ? C7N NAD 1001 A 1 HETATM 40 O O7N NAD . . . G 5 -34.86 22.929 106.286 1 98.95 ? O7N NAD 1001 A 1 HETATM 41 N N7N NAD . . . G 5 -36.749 22.378 105.144 1 98.95 ? N7N NAD 1001 A 1 HETATM 42 C C4N NAD . . . G 5 -36.717 25.632 105.894 1 98.95 ? C4N NAD 1001 A 1 HETATM 43 C C5N NAD . . . G 5 -37.42 26.692 106.52 1 98.95 ? C5N NAD 1001 A 1 HETATM 44 C C6N NAD . . . G 5 -38.135 26.642 107.699 1 98.95 ? C6N NAD 1001 A 1 # _model_server_stats.io_time_ms 141 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 44 #