data_4DYD # _model_server_result.job_id OuC3dMO-VhgqjWKq0lVtQQ _model_server_result.datetime_utc '2025-02-05 14:12:26' _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 4dyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4DYD # _exptl.entry_id 4DYD _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 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 4DYD _cell.length_a 100.48 _cell.length_b 100.48 _cell.length_c 131.91 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 2 2' # _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,D,E,F,G,H,I,J,K,L,M,N,O,P _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' 10_665 -y+1,-x+1,-z+2/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 50.24 87.018233 87.94 # _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 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 4DYD _atom_sites.fract_transf_matrix[1][1] 0.009952 _atom_sites.fract_transf_matrix[1][2] 0.005746 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011492 _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] 0.007581 _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 NAD A 1 301 350 NAD NAD . C 3 GOL A 1 302 401 GOL GOL . D 3 GOL A 1 303 402 GOL GOL . E 3 GOL A 1 304 403 GOL GOL . F 3 GOL A 1 305 404 GOL GOL . G 3 GOL A 1 306 405 GOL GOL . H 3 GOL A 1 307 406 GOL GOL . I 3 GOL A 1 308 407 GOL GOL . J 3 GOL A 1 309 408 GOL GOL . K 3 GOL A 1 310 409 GOL GOL . L 3 GOL A 1 311 410 GOL GOL . M 4 SO4 A 1 312 501 SO4 SO4 . N 5 PO4 A 1 313 521 PO4 PO4 . O 5 PO4 A 1 314 522 PO4 PO4 . P 6 HOH A 1 401 1 HOH HOH . P 6 HOH A 2 402 2 HOH HOH . P 6 HOH A 3 403 3 HOH HOH . P 6 HOH A 4 404 4 HOH HOH . P 6 HOH A 5 405 5 HOH HOH . P 6 HOH A 6 406 6 HOH HOH . P 6 HOH A 7 407 7 HOH HOH . P 6 HOH A 8 408 8 HOH HOH . P 6 HOH A 9 409 9 HOH HOH . P 6 HOH A 10 410 10 HOH HOH . P 6 HOH A 11 411 11 HOH HOH . P 6 HOH A 12 412 12 HOH HOH . P 6 HOH A 13 413 13 HOH HOH . P 6 HOH A 14 414 14 HOH HOH . P 6 HOH A 15 415 15 HOH HOH . P 6 HOH A 16 416 16 HOH HOH . P 6 HOH A 17 417 17 HOH HOH . P 6 HOH A 18 418 18 HOH HOH . P 6 HOH A 19 419 19 HOH HOH . P 6 HOH A 20 420 20 HOH HOH . P 6 HOH A 21 421 21 HOH HOH . P 6 HOH A 22 422 22 HOH HOH . P 6 HOH A 23 423 23 HOH HOH . P 6 HOH A 24 424 24 HOH HOH . P 6 HOH A 25 425 25 HOH HOH . P 6 HOH A 26 426 26 HOH HOH . P 6 HOH A 27 427 27 HOH HOH . P 6 HOH A 28 428 28 HOH HOH . P 6 HOH A 29 429 29 HOH HOH . P 6 HOH A 30 430 30 HOH HOH . P 6 HOH A 31 431 31 HOH HOH . P 6 HOH A 32 432 32 HOH HOH . P 6 HOH A 33 433 33 HOH HOH . P 6 HOH A 34 434 34 HOH HOH . P 6 HOH A 35 435 35 HOH HOH . P 6 HOH A 36 436 36 HOH HOH . P 6 HOH A 37 437 37 HOH HOH . P 6 HOH A 38 438 38 HOH HOH . P 6 HOH A 39 439 39 HOH HOH . P 6 HOH A 40 440 40 HOH HOH . P 6 HOH A 41 441 41 HOH HOH . P 6 HOH A 42 442 42 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 . . . B 2 39.333 31.497 71.153 1 52.66 ? PA NAD 301 A 1 HETATM 2 O O1A NAD . . . B 2 39.472 32.96 71.324 1 69.56 ? O1A NAD 301 A 1 HETATM 3 O O2A NAD . . . B 2 40.482 30.721 70.634 1 71.13 ? O2A NAD 301 A 1 HETATM 4 O O5B NAD . . . B 2 38.855 30.846 72.547 1 59.52 ? O5B NAD 301 A 1 HETATM 5 C C5B NAD . . . B 2 39.335 29.563 72.963 1 45.44 ? C5B NAD 301 A 1 HETATM 6 C C4B NAD . . . B 2 38.358 28.961 73.976 1 53.39 ? C4B NAD 301 A 1 HETATM 7 O O4B NAD . . . B 2 38.922 27.739 74.491 1 60.69 ? O4B NAD 301 A 1 HETATM 8 C C3B NAD . . . B 2 38.24 29.888 75.176 1 55.18 ? C3B NAD 301 A 1 HETATM 9 O O3B NAD . . . B 2 37.028 29.593 75.884 1 47.74 ? O3B NAD 301 A 1 HETATM 10 C C2B NAD . . . B 2 39.429 29.43 75.998 1 65.36 ? C2B NAD 301 A 1 HETATM 11 O O2B NAD . . . B 2 39.272 29.847 77.362 1 54.59 ? O2B NAD 301 A 1 HETATM 12 C C1B NAD . . . B 2 39.136 27.946 75.897 1 50.9 ? C1B NAD 301 A 1 HETATM 13 N N9A NAD . . . B 2 40.209 27.099 76.465 1 104.3 ? N9A NAD 301 A 1 HETATM 14 C C8A NAD . . . B 2 41.45 27.486 76.744 1 68.3 ? C8A NAD 301 A 1 HETATM 15 N N7A NAD . . . B 2 42.118 26.421 77.177 1 56 ? N7A NAD 301 A 1 HETATM 16 C C5A NAD . . . B 2 41.289 25.38 77.174 1 90.56 ? C5A NAD 301 A 1 HETATM 17 C C6A NAD . . . B 2 41.46 24.121 77.568 1 79.85 ? C6A NAD 301 A 1 HETATM 18 N N6A NAD . . . B 2 42.66 23.811 78.052 1 170.81 ? N6A NAD 301 A 1 HETATM 19 N N1A NAD . . . B 2 40.462 23.227 77.541 1 96.34 ? N1A NAD 301 A 1 HETATM 20 C C2A NAD . . . B 2 39.205 23.635 77.083 1 67.25 ? C2A NAD 301 A 1 HETATM 21 N N3A NAD . . . B 2 39.059 24.965 76.672 1 78.37 ? N3A NAD 301 A 1 HETATM 22 C C4A NAD . . . B 2 40.106 25.799 76.73 1 76.92 ? C4A NAD 301 A 1 HETATM 23 O O3 NAD . . . B 2 38.072 31.231 70.19 1 116.92 ? O3 NAD 301 A 1 HETATM 24 P PN NAD . . . B 2 38.308 30.872 68.639 1 71.77 ? PN NAD 301 A 1 HETATM 25 O O1N NAD . . . B 2 39.646 31.354 68.23 1 88.86 ? O1N NAD 301 A 1 HETATM 26 O O2N NAD . . . B 2 37.127 31.31 67.861 1 200.68 ? O2N NAD 301 A 1 HETATM 27 O O5D NAD . . . B 2 38.339 29.262 68.659 1 75.93 ? O5D NAD 301 A 1 HETATM 28 C C5D NAD . . . B 2 39.515 28.566 68.236 1 67.74 ? C5D NAD 301 A 1 HETATM 29 C C4D NAD . . . B 2 39.114 27.216 67.638 1 64.47 ? C4D NAD 301 A 1 HETATM 30 O O4D NAD . . . B 2 38.167 27.476 66.586 1 61.71 ? O4D NAD 301 A 1 HETATM 31 C C3D NAD . . . B 2 40.322 26.631 66.927 1 72.89 ? C3D NAD 301 A 1 HETATM 32 O O3D NAD . . . B 2 40.061 25.277 66.528 1 83.7 ? O3D NAD 301 A 1 HETATM 33 C C2D NAD . . . B 2 40.348 27.533 65.709 1 86.21 ? C2D NAD 301 A 1 HETATM 34 O O2D NAD . . . B 2 41.151 26.955 64.669 1 62.44 ? O2D NAD 301 A 1 HETATM 35 C C1D NAD . . . B 2 38.88 27.43 65.337 1 86.86 ? C1D NAD 301 A 1 HETATM 36 N N1N NAD . . . B 2 38.453 28.465 64.368 1 60.01 ? N1N NAD 301 A 1 HETATM 37 C C2N NAD . . . B 2 38.686 29.82 64.634 1 73 ? C2N NAD 301 A 1 HETATM 38 C C3N NAD . . . B 2 38.386 30.777 63.671 1 95.08 ? C3N NAD 301 A 1 HETATM 39 C C7N NAD . . . B 2 38.513 32.13 63.969 1 162.82 ? C7N NAD 301 A 1 HETATM 40 O O7N NAD . . . B 2 38.17 32.991 63.16 1 63.39 ? O7N NAD 301 A 1 HETATM 41 N N7N NAD . . . B 2 38.986 32.399 65.182 1 67.4 ? N7N NAD 301 A 1 HETATM 42 C C4N NAD . . . B 2 37.857 30.387 62.445 1 89.95 ? C4N NAD 301 A 1 HETATM 43 C C5N NAD . . . B 2 37.598 29.046 62.184 1 55.51 ? C5N NAD 301 A 1 HETATM 44 C C6N NAD . . . B 2 37.894 28.082 63.142 1 53.06 ? C6N NAD 301 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #