data_1M8J # _model_server_result.job_id MVjgRjPH1BBDLo0jhjwAYQ _model_server_result.datetime_utc '2025-04-26 22:48:57' _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 1m8j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1339}' # _entry.id 1M8J # _exptl.entry_id 1M8J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _entity.pdbx_number_of_molecules 1 _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 1M8J _cell.length_a 91.418 _cell.length_b 91.418 _cell.length_c 107.755 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1M8J _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA,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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 91.418 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 45.709 79.17031 0 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 45.709 79.17031 53.8775 5 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 91.418 0 53.8775 6 'crystal symmetry operation' 12_555 x,x-y,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 53.8775 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 1M8J _atom_sites.fract_transf_matrix[1][1] 0.010939 _atom_sites.fract_transf_matrix[1][2] 0.006315 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012631 _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] 0.00928 _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 B 2 SO4 A 1 1759 1759 SO4 SO4 . C 3 NAD A 1 1339 1339 NAD NAD . D 4 HOH A 1 1002 1002 HOH HOH . D 4 HOH A 2 1003 1003 HOH HOH . D 4 HOH A 3 1004 1004 HOH HOH . D 4 HOH A 4 1005 1005 HOH HOH . D 4 HOH A 5 1006 1006 HOH HOH . D 4 HOH A 6 1007 1007 HOH HOH . D 4 HOH A 7 1008 1008 HOH HOH . D 4 HOH A 8 1009 1009 HOH HOH . D 4 HOH A 9 1010 1010 HOH HOH . D 4 HOH A 10 1011 1011 HOH HOH . D 4 HOH A 11 1012 1012 HOH HOH . D 4 HOH A 12 1013 1013 HOH HOH . D 4 HOH A 13 1014 1014 HOH HOH . D 4 HOH A 14 1015 1015 HOH HOH . D 4 HOH A 15 1016 1016 HOH HOH . D 4 HOH A 16 1017 1017 HOH HOH . D 4 HOH A 17 1018 1018 HOH HOH . D 4 HOH A 18 1019 1019 HOH HOH . D 4 HOH A 19 1020 1020 HOH HOH . D 4 HOH A 20 1021 1021 HOH HOH . D 4 HOH A 21 1022 1022 HOH HOH . D 4 HOH A 22 1024 1024 HOH HOH . D 4 HOH A 23 1025 1025 HOH HOH . D 4 HOH A 24 1026 1026 HOH HOH . D 4 HOH A 25 1027 1027 HOH HOH . D 4 HOH A 26 1028 1028 HOH HOH . D 4 HOH A 27 1030 1030 HOH HOH . D 4 HOH A 28 1031 1031 HOH HOH . D 4 HOH A 29 1032 1032 HOH HOH . D 4 HOH A 30 1033 1033 HOH HOH . D 4 HOH A 31 1034 1034 HOH HOH . D 4 HOH A 32 1035 1035 HOH HOH . D 4 HOH A 33 1036 1036 HOH HOH . D 4 HOH A 34 1037 1037 HOH HOH . D 4 HOH A 35 1038 1038 HOH HOH . D 4 HOH A 36 1039 1039 HOH HOH . D 4 HOH A 37 1040 1040 HOH HOH . D 4 HOH A 38 1041 1041 HOH HOH . D 4 HOH A 39 1042 1042 HOH HOH . D 4 HOH A 40 1043 1043 HOH HOH . D 4 HOH A 41 1044 1044 HOH HOH . D 4 HOH A 42 1045 1045 HOH HOH . D 4 HOH A 43 1046 1046 HOH HOH . D 4 HOH A 44 1047 1047 HOH HOH . D 4 HOH A 45 1048 1048 HOH HOH . D 4 HOH A 46 1049 1049 HOH HOH . D 4 HOH A 47 1050 1050 HOH HOH . D 4 HOH A 48 1051 1051 HOH HOH . D 4 HOH A 49 1052 1052 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 . . . C 3 28.434 20.169 43.669 1 38.18 ? PA NAD 1339 A 1 HETATM 2 O O1A NAD . . . C 3 28.286 18.802 43.098 1 37.43 ? O1A NAD 1339 A 1 HETATM 3 O O2A NAD . . . C 3 29.162 20.267 44.961 1 38.81 ? O2A NAD 1339 A 1 HETATM 4 O O5B NAD . . . C 3 26.995 20.868 43.838 1 40.52 ? O5B NAD 1339 A 1 HETATM 5 C C5B NAD . . . C 3 26.027 20.729 42.77 1 43.34 ? C5B NAD 1339 A 1 HETATM 6 C C4B NAD . . . C 3 24.644 21.167 43.228 1 45.5 ? C4B NAD 1339 A 1 HETATM 7 O O4B NAD . . . C 3 24.189 20.192 44.19 1 46.48 ? O4B NAD 1339 A 1 HETATM 8 C C3B NAD . . . C 3 24.577 22.532 43.92 1 47.42 ? C3B NAD 1339 A 1 HETATM 9 O O3B NAD . . . C 3 23.548 23.332 43.303 1 47.93 ? O3B NAD 1339 A 1 HETATM 10 C C2B NAD . . . C 3 24.352 22.138 45.384 1 47.72 ? C2B NAD 1339 A 1 HETATM 11 O O2B NAD . . . C 3 23.629 23.167 46.105 1 47.95 ? O2B NAD 1339 A 1 HETATM 12 C C1B NAD . . . C 3 23.529 20.869 45.214 1 47.63 ? C1B NAD 1339 A 1 HETATM 13 N N9A NAD . . . C 3 23.507 19.973 46.364 1 48.9 ? N9A NAD 1339 A 1 HETATM 14 C C8A NAD . . . C 3 24.521 19.185 46.82 1 49.48 ? C8A NAD 1339 A 1 HETATM 15 N N7A NAD . . . C 3 24.211 18.472 47.898 1 50.86 ? N7A NAD 1339 A 1 HETATM 16 C C5A NAD . . . C 3 22.903 18.825 48.157 1 50.24 ? C5A NAD 1339 A 1 HETATM 17 C C6A NAD . . . C 3 22.013 18.41 49.169 1 51.28 ? C6A NAD 1339 A 1 HETATM 18 N N6A NAD . . . C 3 22.28 17.546 50.127 1 50.66 ? N6A NAD 1339 A 1 HETATM 19 N N1A NAD . . . C 3 20.747 18.951 49.167 1 50.91 ? N1A NAD 1339 A 1 HETATM 20 C C2A NAD . . . C 3 20.441 19.861 48.176 1 51.17 ? C2A NAD 1339 A 1 HETATM 21 N N3A NAD . . . C 3 21.179 20.322 47.187 1 49.77 ? N3A NAD 1339 A 1 HETATM 22 C C4A NAD . . . C 3 22.439 19.752 47.227 1 50.07 ? C4A NAD 1339 A 1 HETATM 23 O O3 NAD . . . C 3 29.128 21.066 42.614 1 39.66 ? O3 NAD 1339 A 1 HETATM 24 P PN NAD . . . C 3 29.464 22.677 42.624 1 40 ? PN NAD 1339 A 1 HETATM 25 O O1N NAD . . . C 3 28.267 23.363 43.128 1 41.46 ? O1N NAD 1339 A 1 HETATM 26 O O2N NAD . . . C 3 30.679 22.913 43.446 1 42.43 ? O2N NAD 1339 A 1 HETATM 27 O O5D NAD . . . C 3 29.624 22.873 41.067 1 40.93 ? O5D NAD 1339 A 1 HETATM 28 C C5D NAD . . . C 3 30.906 23.328 40.738 1 38.47 ? C5D NAD 1339 A 1 HETATM 29 C C4D NAD . . . C 3 31.138 23.339 39.274 1 35.34 ? C4D NAD 1339 A 1 HETATM 30 O O4D NAD . . . C 3 30.934 24.696 38.717 1 33.97 ? O4D NAD 1339 A 1 HETATM 31 C C3D NAD . . . C 3 32.564 22.982 38.998 1 33.1 ? C3D NAD 1339 A 1 HETATM 32 O O3D NAD . . . C 3 32.687 22.179 37.83 1 34.95 ? O3D NAD 1339 A 1 HETATM 33 C C2D NAD . . . C 3 33.152 24.352 38.852 1 32.95 ? C2D NAD 1339 A 1 HETATM 34 O O2D NAD . . . C 3 34.455 24.263 38.283 1 32.56 ? O2D NAD 1339 A 1 HETATM 35 C C1D NAD . . . C 3 32.091 24.976 37.971 1 31.67 ? C1D NAD 1339 A 1 HETATM 36 N N1N NAD . . . C 3 32.327 26.415 37.761 1 30.99 ? N1N NAD 1339 A 1 HETATM 37 C C2N NAD . . . C 3 33.278 26.821 36.827 1 30 ? C2N NAD 1339 A 1 HETATM 38 C C3N NAD . . . C 3 33.679 28.236 36.675 1 29.88 ? C3N NAD 1339 A 1 HETATM 39 C C7N NAD . . . C 3 34.779 28.505 35.73 1 31.67 ? C7N NAD 1339 A 1 HETATM 40 O O7N NAD . . . C 3 35.143 29.684 35.605 1 26.26 ? O7N NAD 1339 A 1 HETATM 41 N N7N NAD . . . C 3 35.385 27.539 35.016 1 29.38 ? N7N NAD 1339 A 1 HETATM 42 C C4N NAD . . . C 3 32.894 29.298 37.417 1 27.78 ? C4N NAD 1339 A 1 HETATM 43 C C5N NAD . . . C 3 31.852 28.709 38.322 1 30.39 ? C5N NAD 1339 A 1 HETATM 44 C C6N NAD . . . C 3 31.613 27.416 38.488 1 30.44 ? C6N NAD 1339 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 44 #