data_3WMX # _model_server_result.job_id c9ZgshJYevWLZ_3fMjFGmA _model_server_result.datetime_utc '2024-12-12 17:45:05' _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 3wmx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 3WMX # _exptl.entry_id 3WMX _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.47 _cell.angle_gamma 90 _cell.entry_id 3WMX _cell.length_a 91.598 _cell.length_b 88.109 _cell.length_c 113.597 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WMX _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,I,K,M 1 1 B,D,G,H,J,L,N 2 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 ? 2 E N N ? 2 G N N ? 2 I N N ? 2 J 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 3WMX _atom_sites.fract_transf_matrix[1][1] 0.010917 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003022 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01135 _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] 0.009134 _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 2 NAD A 1 401 1 NAD NAD . F 3 THR A 1 402 1 THR THR . G 2 NAD B 1 401 1 NAD NAD . H 3 THR B 1 402 1 THR THR . I 2 NAD C 1 401 1 NAD NAD . J 2 NAD D 1 401 1 NAD NAD . K 4 HOH A 1 501 1 HOH HOH . K 4 HOH A 2 502 2 HOH HOH . K 4 HOH A 3 503 5 HOH HOH . K 4 HOH A 4 504 9 HOH HOH . K 4 HOH A 5 505 10 HOH HOH . K 4 HOH A 6 506 11 HOH HOH . K 4 HOH A 7 507 16 HOH HOH . K 4 HOH A 8 508 22 HOH HOH . K 4 HOH A 9 509 26 HOH HOH . K 4 HOH A 10 510 27 HOH HOH . K 4 HOH A 11 511 28 HOH HOH . K 4 HOH A 12 512 29 HOH HOH . K 4 HOH A 13 513 31 HOH HOH . K 4 HOH A 14 514 32 HOH HOH . K 4 HOH A 15 515 36 HOH HOH . K 4 HOH A 16 516 37 HOH HOH . K 4 HOH A 17 517 38 HOH HOH . K 4 HOH A 18 518 39 HOH HOH . K 4 HOH A 19 519 42 HOH HOH . K 4 HOH A 20 520 43 HOH HOH . K 4 HOH A 21 521 44 HOH HOH . K 4 HOH A 22 522 45 HOH HOH . K 4 HOH A 23 523 46 HOH HOH . K 4 HOH A 24 524 48 HOH HOH . K 4 HOH A 25 525 56 HOH HOH . K 4 HOH A 26 526 57 HOH HOH . K 4 HOH A 27 527 58 HOH HOH . K 4 HOH A 28 528 60 HOH HOH . K 4 HOH A 29 529 65 HOH HOH . K 4 HOH A 30 530 66 HOH HOH . K 4 HOH A 31 531 67 HOH HOH . K 4 HOH A 32 532 68 HOH HOH . K 4 HOH A 33 533 72 HOH HOH . K 4 HOH A 34 534 80 HOH HOH . K 4 HOH A 35 535 83 HOH HOH . L 4 HOH B 1 501 12 HOH HOH . L 4 HOH B 2 502 13 HOH HOH . L 4 HOH B 3 503 17 HOH HOH . L 4 HOH B 4 504 18 HOH HOH . L 4 HOH B 5 505 19 HOH HOH . L 4 HOH B 6 506 20 HOH HOH . L 4 HOH B 7 507 21 HOH HOH . L 4 HOH B 8 508 30 HOH HOH . L 4 HOH B 9 509 33 HOH HOH . L 4 HOH B 10 510 40 HOH HOH . L 4 HOH B 11 511 49 HOH HOH . L 4 HOH B 12 512 54 HOH HOH . L 4 HOH B 13 513 55 HOH HOH . L 4 HOH B 14 514 62 HOH HOH . L 4 HOH B 15 515 63 HOH HOH . L 4 HOH B 16 516 74 HOH HOH . L 4 HOH B 17 517 78 HOH HOH . M 4 HOH C 1 501 3 HOH HOH . M 4 HOH C 2 502 6 HOH HOH . M 4 HOH C 3 503 8 HOH HOH . M 4 HOH C 4 504 41 HOH HOH . M 4 HOH C 5 505 50 HOH HOH . M 4 HOH C 6 506 51 HOH HOH . M 4 HOH C 7 507 59 HOH HOH . M 4 HOH C 8 508 61 HOH HOH . M 4 HOH C 9 509 64 HOH HOH . M 4 HOH C 10 510 69 HOH HOH . M 4 HOH C 11 511 71 HOH HOH . M 4 HOH C 12 512 75 HOH HOH . M 4 HOH C 13 513 77 HOH HOH . M 4 HOH C 14 514 81 HOH HOH . N 4 HOH D 1 501 70 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 NAD . . . I 2 25.994 11.393 29.624 1 31.03 ? PA NAD 401 C 1 HETATM 2 O O1A NAD . . . I 2 26.074 10.006 30.182 1 27.68 ? O1A NAD 401 C 1 HETATM 3 O O2A NAD . . . I 2 26.651 11.773 28.325 1 33.7 ? O2A NAD 401 C 1 HETATM 4 O O5B NAD . . . I 2 26.581 12.355 30.759 1 31.84 ? O5B NAD 401 C 1 HETATM 5 C C5B NAD . . . I 2 26.38 12.058 32.132 1 28.75 ? C5B NAD 401 C 1 HETATM 6 C C4B NAD . . . I 2 27.373 12.902 32.93 1 32.36 ? C4B NAD 401 C 1 HETATM 7 O O4B NAD . . . I 2 27.031 12.927 34.317 1 32.59 ? O4B NAD 401 C 1 HETATM 8 C C3B NAD . . . I 2 28.791 12.345 32.87 1 30.87 ? C3B NAD 401 C 1 HETATM 9 O O3B NAD . . . I 2 29.697 13.435 32.726 1 29.52 ? O3B NAD 401 C 1 HETATM 10 C C2B NAD . . . I 2 29.007 11.674 34.209 1 27.37 ? C2B NAD 401 C 1 HETATM 11 O O2B NAD . . . I 2 30.376 11.652 34.642 1 28.47 ? O2B NAD 401 C 1 HETATM 12 C C1B NAD . . . I 2 28.191 12.593 35.086 1 27.66 ? C1B NAD 401 C 1 HETATM 13 N N9A NAD . . . I 2 27.868 11.978 36.389 1 31.08 ? N9A NAD 401 C 1 HETATM 14 C C8A NAD . . . I 2 27.631 10.67 36.653 1 32.86 ? C8A NAD 401 C 1 HETATM 15 N N7A NAD . . . I 2 27.371 10.497 37.976 1 34.94 ? N7A NAD 401 C 1 HETATM 16 C C5A NAD . . . I 2 27.448 11.705 38.562 1 27.81 ? C5A NAD 401 C 1 HETATM 17 C C6A NAD . . . I 2 27.284 12.237 39.919 1 30.25 ? C6A NAD 401 C 1 HETATM 18 N N6A NAD . . . I 2 26.983 11.393 40.94 1 30.98 ? N6A NAD 401 C 1 HETATM 19 N N1A NAD . . . I 2 27.432 13.574 40.111 1 27.34 ? N1A NAD 401 C 1 HETATM 20 C C2A NAD . . . I 2 27.72 14.393 39.097 1 25.23 ? C2A NAD 401 C 1 HETATM 21 N N3A NAD . . . I 2 27.888 13.971 37.836 1 23.32 ? N3A NAD 401 C 1 HETATM 22 C C4A NAD . . . I 2 27.767 12.672 37.517 1 28.72 ? C4A NAD 401 C 1 HETATM 23 O O3 NAD . . . I 2 24.454 11.829 29.508 1 29.57 ? O3 NAD 401 C 1 HETATM 24 P PN NAD . . . I 2 23.899 12.961 28.508 1 32.16 ? PN NAD 401 C 1 HETATM 25 O O1N NAD . . . I 2 24.787 14.186 28.578 1 33.75 ? O1N NAD 401 C 1 HETATM 26 O O2N NAD . . . I 2 23.541 12.286 27.194 1 26.59 ? O2N NAD 401 C 1 HETATM 27 O O5D NAD . . . I 2 22.492 13.296 29.184 1 28.1 ? O5D NAD 401 C 1 HETATM 28 C C5D NAD . . . I 2 22.378 14.227 30.243 1 28.44 ? C5D NAD 401 C 1 HETATM 29 C C4D NAD . . . I 2 20.888 14.286 30.585 1 31.54 ? C4D NAD 401 C 1 HETATM 30 O O4D NAD . . . I 2 20.074 14.246 29.386 1 27.85 ? O4D NAD 401 C 1 HETATM 31 C C3D NAD . . . I 2 20.447 13.108 31.444 1 27.03 ? C3D NAD 401 C 1 HETATM 32 O O3D NAD . . . I 2 19.537 13.582 32.45 1 27.76 ? O3D NAD 401 C 1 HETATM 33 C C2D NAD . . . I 2 19.754 12.207 30.445 1 26.78 ? C2D NAD 401 C 1 HETATM 34 O O2D NAD . . . I 2 18.736 11.428 31.034 1 23.04 ? O2D NAD 401 C 1 HETATM 35 C C1D NAD . . . I 2 19.128 13.193 29.493 1 26.03 ? C1D NAD 401 C 1 HETATM 36 N N1N NAD . . . I 2 18.813 12.637 28.177 1 33.97 ? N1N NAD 401 C 1 HETATM 37 C C2N NAD . . . I 2 19.773 12.413 27.267 1 35.55 ? C2N NAD 401 C 1 HETATM 38 C C3N NAD . . . I 2 19.453 11.908 25.997 1 34.45 ? C3N NAD 401 C 1 HETATM 39 C C7N NAD . . . I 2 20.51 11.649 24.942 1 31.25 ? C7N NAD 401 C 1 HETATM 40 O O7N NAD . . . I 2 20.179 11.124 23.894 1 31.53 ? O7N NAD 401 C 1 HETATM 41 N N7N NAD . . . I 2 21.782 11.988 25.141 1 29.05 ? N7N NAD 401 C 1 HETATM 42 C C4N NAD . . . I 2 18.119 11.638 25.701 1 31.82 ? C4N NAD 401 C 1 HETATM 43 C C5N NAD . . . I 2 17.147 11.888 26.651 1 32.26 ? C5N NAD 401 C 1 HETATM 44 C C6N NAD . . . I 2 17.519 12.4 27.886 1 33.23 ? C6N NAD 401 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #