data_4Y9D # _model_server_result.job_id wye2d39AMN3Df76zCn75kw _model_server_result.datetime_utc '2024-11-14 06:47:33' _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 4y9d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4Y9D # _exptl.entry_id 4Y9D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 665.441 _entity.id 2 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description '1,4-DIHYDRONICOTINAMIDE 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 4Y9D _cell.length_a 61.762 _cell.length_b 61.762 _cell.length_c 134.713 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y9D _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -89.808667 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C21 H29 N7 O14 P2' _chem_comp.formula_weight 665.441 _chem_comp.id NAI _chem_comp.mon_nstd_flag . _chem_comp.name '1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms NADH # 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 NAI doub 237 n n PA O2A NAI sing 238 n n PA O5B NAI sing 239 n n PA O3 NAI sing 240 n n O2A HOA2 NAI sing 241 n n O5B C5B NAI sing 242 n n C5B C4B NAI sing 243 n n C5B H51A NAI sing 244 n n C5B H52A NAI sing 245 n n C4B O4B NAI sing 246 n n C4B C3B NAI sing 247 n n C4B H4B NAI sing 248 n n O4B C1B NAI sing 249 n n C3B O3B NAI sing 250 n n C3B C2B NAI sing 251 n n C3B H3B NAI sing 252 n n O3B HO3A NAI sing 253 n n C2B O2B NAI sing 254 n n C2B C1B NAI sing 255 n n C2B H2B NAI sing 256 n n O2B HO2A NAI sing 257 n n C1B N9A NAI sing 258 n n C1B H1B NAI sing 259 n n N9A C8A NAI sing 260 n y N9A C4A NAI sing 261 n y C8A N7A NAI doub 262 n y C8A H8A NAI sing 263 n n N7A C5A NAI sing 264 n y C5A C6A NAI sing 265 n y C5A C4A NAI doub 266 n y C6A N6A NAI sing 267 n n C6A N1A NAI doub 268 n y N6A H61A NAI sing 269 n n N6A H62A NAI sing 270 n n N1A C2A NAI sing 271 n y C2A N3A NAI doub 272 n y C2A H2A NAI sing 273 n n N3A C4A NAI sing 274 n y O3 PN NAI sing 275 n n PN O1N NAI sing 276 n n PN O2N NAI doub 277 n n PN O5D NAI sing 278 n n O1N HO1N NAI sing 279 n n O5D C5D NAI sing 280 n n C5D C4D NAI sing 281 n n C5D H51N NAI sing 282 n n C5D H52N NAI sing 283 n n C4D O4D NAI sing 284 n n C4D C3D NAI sing 285 n n C4D H4D NAI sing 286 n n O4D C1D NAI sing 287 n n C3D O3D NAI sing 288 n n C3D C2D NAI sing 289 n n C3D H3D NAI sing 290 n n O3D HO3N NAI sing 291 n n C2D O2D NAI sing 292 n n C2D C1D NAI sing 293 n n C2D H2D NAI sing 294 n n O2D HO2N NAI sing 295 n n C1D N1N NAI sing 296 n n C1D H1D NAI sing 297 n n N1N C2N NAI sing 298 n n N1N C6N NAI sing 299 n n C2N C3N NAI doub 300 n n C2N H2N NAI sing 301 n n C3N C7N NAI sing 302 n n C3N C4N NAI sing 303 n n C7N O7N NAI doub 304 n n C7N N7N NAI sing 305 n n N7N H71N NAI sing 306 n n N7N H72N NAI sing 307 n n C4N C5N NAI sing 308 n n C4N H4N NAI sing 309 n n C4N H42N NAI sing 310 n n C5N C6N NAI doub 311 n n C5N H5N NAI sing 312 n n C6N H6N NAI sing 313 n n # _atom_sites.entry_id 4Y9D _atom_sites.fract_transf_matrix[1][1] 0.016191 _atom_sites.fract_transf_matrix[1][2] 0.009348 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018696 _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] 0.007423 _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 NAI A 1 401 306 NAI NAD . C 3 HOH A 1 501 11 HOH HOH . C 3 HOH A 2 502 6 HOH HOH . C 3 HOH A 3 503 1 HOH HOH . C 3 HOH A 4 504 7 HOH HOH . C 3 HOH A 5 505 2 HOH HOH . C 3 HOH A 6 506 3 HOH HOH . C 3 HOH A 7 507 4 HOH HOH . C 3 HOH A 8 508 5 HOH HOH . C 3 HOH A 9 509 8 HOH HOH . C 3 HOH A 10 510 9 HOH HOH . C 3 HOH A 11 511 10 HOH HOH . C 3 HOH A 12 512 12 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 NAI . . . B 2 -12.117 25.556 -24.591 1 89.03 ? PA NAI 401 A 1 HETATM 2 O O1A NAI . . . B 2 -10.678 25.4 -24.951 1 89.42 ? O1A NAI 401 A 1 HETATM 3 O O2A NAI . . . B 2 -12.236 26.023 -23.135 1 89.26 ? O2A NAI 401 A 1 HETATM 4 O O5B NAI . . . B 2 -12.891 24.157 -24.738 1 80.38 ? O5B NAI 401 A 1 HETATM 5 C C5B NAI . . . B 2 -12.66 23.332 -25.841 1 76.52 ? C5B NAI 401 A 1 HETATM 6 C C4B NAI . . . B 2 -12.963 21.924 -25.722 1 73.13 ? C4B NAI 401 A 1 HETATM 7 O O4B NAI . . . B 2 -12.862 21.298 -26.993 1 73.33 ? O4B NAI 401 A 1 HETATM 8 C C3B NAI . . . B 2 -11.96 21.271 -24.834 1 72.72 ? C3B NAI 401 A 1 HETATM 9 O O3B NAI . . . B 2 -12.596 20.572 -23.82 1 71.86 ? O3B NAI 401 A 1 HETATM 10 C C2B NAI . . . B 2 -11.252 20.378 -25.671 1 71.7 ? C2B NAI 401 A 1 HETATM 11 O O2B NAI . . . B 2 -10.946 19.229 -25.004 1 71.54 ? O2B NAI 401 A 1 HETATM 12 C C1B NAI . . . B 2 -12.21 20.084 -26.796 1 70.91 ? C1B NAI 401 A 1 HETATM 13 N N9A NAI . . . B 2 -11.522 19.464 -27.96 1 68.27 ? N9A NAI 401 A 1 HETATM 14 C C8A NAI . . . B 2 -10.389 19.871 -28.547 1 66.74 ? C8A NAI 401 A 1 HETATM 15 N N7A NAI . . . B 2 -10.092 19.038 -29.553 1 65.16 ? N7A NAI 401 A 1 HETATM 16 C C5A NAI . . . B 2 -11.045 18.088 -29.614 1 63.73 ? C5A NAI 401 A 1 HETATM 17 C C6A NAI . . . B 2 -11.246 16.991 -30.435 1 63.55 ? C6A NAI 401 A 1 HETATM 18 N N6A NAI . . . B 2 -10.317 16.692 -31.482 1 63.41 ? N6A NAI 401 A 1 HETATM 19 N N1A NAI . . . B 2 -12.324 16.204 -30.248 1 63.19 ? N1A NAI 401 A 1 HETATM 20 C C2A NAI . . . B 2 -13.185 16.483 -29.262 1 65.12 ? C2A NAI 401 A 1 HETATM 21 N N3A NAI . . . B 2 -13.012 17.53 -28.455 1 65.1 ? N3A NAI 401 A 1 HETATM 22 C C4A NAI . . . B 2 -11.952 18.355 -28.605 1 66.52 ? C4A NAI 401 A 1 HETATM 23 O O3 NAI . . . B 2 -12.691 26.624 -25.507 1 90.02 ? O3 NAI 401 A 1 HETATM 24 P PN NAI . . . B 2 -14.191 27.153 -25.352 1 89.94 ? PN NAI 401 A 1 HETATM 25 O O1N NAI . . . B 2 -15.044 26.037 -24.991 1 86.84 ? O1N NAI 401 A 1 HETATM 26 O O2N NAI . . . B 2 -14.66 27.706 -26.635 1 94.1 ? O2N NAI 401 A 1 HETATM 27 O O5D NAI . . . B 2 -14.243 28.278 -24.228 1 103.14 ? O5D NAI 401 A 1 HETATM 28 H H51A NAI . . . B 2 -11.662 23.409 -26.077 1 91.83 ? H51A NAI 401 A 1 HETATM 29 H H52A NAI . . . B 2 -13.182 23.694 -26.604 1 91.83 ? H52A NAI 401 A 1 HETATM 30 H H4B NAI . . . B 2 -13.847 21.827 -25.417 1 87.75 ? H4B NAI 401 A 1 HETATM 31 H H3B NAI . . . B 2 -11.359 21.929 -24.448 1 87.26 ? H3B NAI 401 A 1 HETATM 32 H HO3A NAI . . . B 2 -13.355 21.012 -23.581 1 86.23 ? HO3A NAI 401 A 1 HETATM 33 H H2B NAI . . . B 2 -10.378 20.842 -26.033 1 86.04 ? H2B NAI 401 A 1 HETATM 34 H HO2A NAI . . . B 2 -10.326 18.822 -25.413 1 85.84 ? HO2A NAI 401 A 1 HETATM 35 H H1B NAI . . . B 2 -12.893 19.378 -26.455 1 85.1 ? H1B NAI 401 A 1 HETATM 36 H H8A NAI . . . B 2 -9.854 20.658 -28.278 1 80.09 ? H8A NAI 401 A 1 HETATM 37 H H61A NAI . . . B 2 -10.511 16.021 -32.101 1 76.09 ? H61A NAI 401 A 1 HETATM 38 H H62A NAI . . . B 2 -9.568 17.138 -31.542 1 76.09 ? H62A NAI 401 A 1 HETATM 39 H H2A NAI . . . B 2 -13.938 15.924 -29.134 1 78.15 ? H2A NAI 401 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 39 #