data_1WDM # _model_server_result.job_id dtvUq9HfcJstKunP6ML56A _model_server_result.datetime_utc '2024-11-22 18:05:01' _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":"H","auth_seq_id":2001}' # _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 . . . H 5 -17.813 33.426 147.108 1 123.42 ? PA NAD 2001 B 1 HETATM 2 O O1A NAD . . . H 5 -16.651 33.95 146.333 1 123.42 ? O1A NAD 2001 B 1 HETATM 3 O O2A NAD . . . H 5 -18.292 34.289 148.225 1 123.42 ? O2A NAD 2001 B 1 HETATM 4 O O5B NAD . . . H 5 -19.052 33.219 146.115 1 123.42 ? O5B NAD 2001 B 1 HETATM 5 C C5B NAD . . . H 5 -20.279 32.63 146.557 1 123.42 ? C5B NAD 2001 B 1 HETATM 6 C C4B NAD . . . H 5 -21.073 32.132 145.369 1 123.42 ? C4B NAD 2001 B 1 HETATM 7 O O4B NAD . . . H 5 -22.143 31.254 145.848 1 123.42 ? O4B NAD 2001 B 1 HETATM 8 C C3B NAD . . . H 5 -21.791 33.252 144.605 1 123.42 ? C3B NAD 2001 B 1 HETATM 9 O O3B NAD . . . H 5 -21.776 33.012 143.197 1 123.42 ? O3B NAD 2001 B 1 HETATM 10 C C2B NAD . . . H 5 -23.216 33.201 145.161 1 123.42 ? C2B NAD 2001 B 1 HETATM 11 O O2B NAD . . . H 5 -24.188 33.738 144.286 1 123.42 ? O2B NAD 2001 B 1 HETATM 12 C C1B NAD . . . H 5 -23.379 31.694 145.314 1 123.42 ? C1B NAD 2001 B 1 HETATM 13 N N9A NAD . . . H 5 -24.465 31.325 146.236 1 123.42 ? N9A NAD 2001 B 1 HETATM 14 C C8A NAD . . . H 5 -24.716 31.799 147.509 1 123.42 ? C8A NAD 2001 B 1 HETATM 15 N N7A NAD . . . H 5 -25.775 31.27 148.079 1 123.42 ? N7A NAD 2001 B 1 HETATM 16 C C5A NAD . . . H 5 -26.258 30.381 147.127 1 123.42 ? C5A NAD 2001 B 1 HETATM 17 C C6A NAD . . . H 5 -27.378 29.497 147.098 1 123.42 ? C6A NAD 2001 B 1 HETATM 18 N N6A NAD . . . H 5 -28.231 29.357 148.114 1 123.42 ? N6A NAD 2001 B 1 HETATM 19 N N1A NAD . . . H 5 -27.582 28.733 145.968 1 123.42 ? N1A NAD 2001 B 1 HETATM 20 C C2A NAD . . . H 5 -26.725 28.86 144.926 1 123.42 ? C2A NAD 2001 B 1 HETATM 21 N N3A NAD . . . H 5 -25.642 29.661 144.836 1 123.42 ? N3A NAD 2001 B 1 HETATM 22 C C4A NAD . . . H 5 -25.464 30.409 145.977 1 123.42 ? C4A NAD 2001 B 1 HETATM 23 O O3 NAD . . . H 5 -17.382 32.005 147.721 1 123.42 ? O3 NAD 2001 B 1 HETATM 24 P PN NAD . . . H 5 -16.684 30.87 146.814 1 123.42 ? PN NAD 2001 B 1 HETATM 25 O O1N NAD . . . H 5 -17.28 30.908 145.446 1 123.42 ? O1N NAD 2001 B 1 HETATM 26 O O2N NAD . . . H 5 -15.211 31.096 146.888 1 123.42 ? O2N NAD 2001 B 1 HETATM 27 O O5D NAD . . . H 5 -16.994 29.436 147.441 1 123.42 ? O5D NAD 2001 B 1 HETATM 28 C C5D NAD . . . H 5 -16.969 29.222 148.856 1 123.42 ? C5D NAD 2001 B 1 HETATM 29 C C4D NAD . . . H 5 -16.717 27.76 149.157 1 123.42 ? C4D NAD 2001 B 1 HETATM 30 O O4D NAD . . . H 5 -15.373 27.424 148.695 1 123.42 ? O4D NAD 2001 B 1 HETATM 31 C C3D NAD . . . H 5 -16.721 27.454 150.655 1 123.42 ? C3D NAD 2001 B 1 HETATM 32 O O3D NAD . . . H 5 -17.305 26.175 150.916 1 123.42 ? O3D NAD 2001 B 1 HETATM 33 C C2D NAD . . . H 5 -15.234 27.474 151.024 1 123.42 ? C2D NAD 2001 B 1 HETATM 34 O O2D NAD . . . H 5 -14.921 26.702 152.165 1 123.42 ? O2D NAD 2001 B 1 HETATM 35 C C1D NAD . . . H 5 -14.606 26.883 149.763 1 123.42 ? C1D NAD 2001 B 1 HETATM 36 N N1N NAD . . . H 5 -13.16 27.19 149.678 1 123.42 ? N1N NAD 2001 B 1 HETATM 37 C C2N NAD . . . H 5 -12.747 28.508 149.466 1 123.42 ? C2N NAD 2001 B 1 HETATM 38 C C3N NAD . . . H 5 -11.397 28.818 149.383 1 123.42 ? C3N NAD 2001 B 1 HETATM 39 C C7N NAD . . . H 5 -10.914 30.303 149.155 1 123.42 ? C7N NAD 2001 B 1 HETATM 40 O O7N NAD . . . H 5 -10.83 30.76 148.02 1 123.42 ? O7N NAD 2001 B 1 HETATM 41 N N7N NAD . . . H 5 -10.614 30.995 150.274 1 123.42 ? N7N NAD 2001 B 1 HETATM 42 C C4N NAD . . . H 5 -10.377 27.804 149.511 1 123.42 ? C4N NAD 2001 B 1 HETATM 43 C C5N NAD . . . H 5 -10.892 26.495 149.717 1 123.42 ? C5N NAD 2001 B 1 HETATM 44 C C6N NAD . . . H 5 -12.218 26.122 149.808 1 123.42 ? C6N NAD 2001 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 44 #