data_1GZU # _model_server_result.job_id ppcdjBrkp08EEVfg5faZRQ _model_server_result.datetime_utc '2024-12-05 13:35:03' _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 1gzu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 1GZU # _exptl.entry_id 1GZU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 335.227 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE' _entity.pdbx_number_of_molecules 3 _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 90 _cell.entry_id 1GZU _cell.length_a 140.8 _cell.length_b 235.7 _cell.length_c 89 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GZU _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 44.5 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F 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 covale ? covale1 A C ASN 33 A ASN 22 1_555 A N MSE 34 A MSE 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C MSE 34 A MSE 23 1_555 A N HIS 35 A HIS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale3 A C TYR 45 A TYR 34 1_555 A N MSE 46 A MSE 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale4 A C MSE 46 A MSE 35 1_555 A N ASN 47 A ASN 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C ILE 79 A ILE 68 1_555 A N MSE 80 A MSE 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 A C MSE 80 A MSE 69 1_555 A N ALA 81 A ALA 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale7 B C ASN 33 B ASN 22 1_555 B N MSE 34 B MSE 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale8 B C MSE 34 B MSE 23 1_555 B N HIS 35 B HIS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale9 B C TYR 45 B TYR 34 1_555 B N MSE 46 B MSE 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale10 B C MSE 46 B MSE 35 1_555 B N ASN 47 B ASN 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale11 B C ILE 79 B ILE 68 1_555 B N MSE 80 B MSE 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale12 B C MSE 80 B MSE 69 1_555 B N ALA 81 B ALA 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale13 C C ASN 33 C ASN 22 1_555 C N MSE 34 C MSE 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale14 C C MSE 34 C MSE 23 1_555 C N HIS 35 C HIS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale15 C C TYR 45 C TYR 34 1_555 C N MSE 46 C MSE 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 C C MSE 46 C MSE 35 1_555 C N ASN 47 C ASN 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale17 C C ILE 79 C ILE 68 1_555 C N MSE 80 C MSE 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale18 C C MSE 80 C MSE 69 1_555 C N ALA 81 C ALA 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C11 H16 N2 O8 P 1' _chem_comp.formula_weight 335.227 _chem_comp.id NMN _chem_comp.mon_nstd_flag . _chem_comp.name 'BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'NICOTINAMIDE MONONUCLEOTIDE' # 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 O3P P NMN doub 235 n n P O1P NMN sing 236 n n P O2P NMN sing 237 n n P O5R NMN sing 238 n n O1P H1PO NMN sing 239 n n O2P H2PO NMN sing 240 n n O5R C5R NMN sing 241 n n C5R C4R NMN sing 242 n n C5R H5R1 NMN sing 243 n n C5R H5R2 NMN sing 244 n n C4R O4R NMN sing 245 n n C4R C3R NMN sing 246 n n C4R H4RC NMN sing 247 n n O4R C1R NMN sing 248 n n C3R O3R NMN sing 249 n n C3R C2R NMN sing 250 n n C3R H3RC NMN sing 251 n n O3R H3RO NMN sing 252 n n C2R O2R NMN sing 253 n n C2R C1R NMN sing 254 n n C2R H2RC NMN sing 255 n n O2R H2RO NMN sing 256 n n C1R N1 NMN sing 257 n n C1R H1RC NMN sing 258 n n N1 C2 NMN doub 259 n y N1 C6 NMN sing 260 n y C2 C3 NMN sing 261 n y C2 HC2 NMN sing 262 n n C3 C7 NMN sing 263 n n C3 C4 NMN doub 264 n y C7 O7 NMN doub 265 n n C7 N7 NMN sing 266 n n N7 HN71 NMN sing 267 n n N7 HN72 NMN sing 268 n n C4 C5 NMN sing 269 n y C4 HC4 NMN sing 270 n n C5 C6 NMN doub 271 n y C5 HC5 NMN sing 272 n n C6 HC6 NMN sing 273 n n # _atom_sites.entry_id 1GZU _atom_sites.fract_transf_matrix[1][1] 0.007102 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004243 _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] 0.011236 _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 D 2 NMN A 1 501 501 NMN NMN . E 2 NMN B 1 501 501 NMN NMN . F 2 NMN C 1 501 501 NMN NMN . # 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 O3P NMN . . . D 2 -19.277 61.183 37.189 1 46.69 ? O3P NMN 501 A 1 HETATM 2 P P NMN . . . D 2 -17.917 61.023 37.797 1 54.6 ? P NMN 501 A 1 HETATM 3 O O1P NMN . . . D 2 -16.973 60.986 36.62 1 55.26 ? O1P NMN 501 A 1 HETATM 4 O O2P NMN . . . D 2 -17.711 62.056 38.908 1 51.22 ? O2P NMN 501 A 1 HETATM 5 O O5R NMN . . . D 2 -17.767 59.578 38.552 1 53.56 ? O5R NMN 501 A 1 HETATM 6 C C5R NMN . . . D 2 -16.497 58.918 38.555 1 51.15 ? C5R NMN 501 A 1 HETATM 7 C C4R NMN . . . D 2 -16.399 57.846 39.606 1 50.83 ? C4R NMN 501 A 1 HETATM 8 O O4R NMN . . . D 2 -15.164 57.199 40.014 1 51.6 ? O4R NMN 501 A 1 HETATM 9 C C3R NMN . . . D 2 -17.378 57.492 40.394 1 53.17 ? C3R NMN 501 A 1 HETATM 10 O O3R NMN . . . D 2 -18.421 57.12 39.913 1 56.78 ? O3R NMN 501 A 1 HETATM 11 C C2R NMN . . . D 2 -16.861 56.914 41.487 1 50.56 ? C2R NMN 501 A 1 HETATM 12 O O2R NMN . . . D 2 -17.552 56.291 42.287 1 39.33 ? O2R NMN 501 A 1 HETATM 13 C C1R NMN . . . D 2 -15.513 56.836 41.369 1 50.21 ? C1R NMN 501 A 1 HETATM 14 N N1 NMN . . . D 2 -14.578 56.903 42.392 1 47.26 ? N1 NMN 501 A 1 HETATM 15 C C2 NMN . . . D 2 -14.05 55.768 42.876 1 46 ? C2 NMN 501 A 1 HETATM 16 C C3 NMN . . . D 2 -13.108 55.766 43.898 1 45.75 ? C3 NMN 501 A 1 HETATM 17 C C7 NMN . . . D 2 -12.583 54.463 44.402 1 51.32 ? C7 NMN 501 A 1 HETATM 18 O O7 NMN . . . D 2 -12.964 53.419 43.91 1 50.01 ? O7 NMN 501 A 1 HETATM 19 N N7 NMN . . . D 2 -11.679 54.473 45.371 1 59.47 ? N7 NMN 501 A 1 HETATM 20 C C4 NMN . . . D 2 -12.657 56.96 44.437 1 43.8 ? C4 NMN 501 A 1 HETATM 21 C C5 NMN . . . D 2 -13.19 58.134 43.915 1 45.88 ? C5 NMN 501 A 1 HETATM 22 C C6 NMN . . . D 2 -14.157 58.081 42.894 1 46.09 ? C6 NMN 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 383 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #