data_4NMZ # _model_server_result.job_id sb5I9jJjhpIebuU52XkRTw _model_server_result.datetime_utc '2024-10-11 10:21:53' _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 4nmz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4NMZ # _exptl.entry_id 4NMZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-3',5'-DIPHOSPHATE" _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 94.43 _cell.angle_gamma 90 _cell.entry_id 4NMZ _cell.length_a 31.07 _cell.length_b 60.422 _cell.length_c 38.333 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NMZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # _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 # 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 OD2 ASP 21 A ASP 21 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc5 B O5P THP . A THP 201 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.162 ? metalc ? metalc6 C CA CA . A CA 202 1_555 D O HOH . A HOH 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? metalc ? metalc7 C CA CA . A CA 202 1_555 D O HOH . A HOH 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id THP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-3',5'-DIPHOSPHATE" _chem_comp.type 'dna linking' _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 P2 O4P THP doub 277 n n P2 O5P THP sing 278 n n P2 O6P THP sing 279 n n P2 O5' THP sing 280 n n O5P HOP5 THP sing 281 n n O6P HOP6 THP sing 282 n n P1 O1P THP doub 283 n n P1 O2P THP sing 284 n n P1 O3P THP sing 285 n n P1 O3' THP sing 286 n n O2P HOP2 THP sing 287 n n O3P HOP3 THP sing 288 n n O5' C5' THP sing 289 n n C5' C4' THP sing 290 n n C5' "H5'1" THP sing 291 n n C5' "H5'2" THP sing 292 n n C4' O4' THP sing 293 n n C4' C3' THP sing 294 n n C4' H4' THP sing 295 n n O4' C1' THP sing 296 n n C3' O3' THP sing 297 n n C3' C2' THP sing 298 n n C3' H3' THP sing 299 n n C2' C1' THP sing 300 n n C2' "H2'1" THP sing 301 n n C2' "H2'2" THP sing 302 n n C1' N1 THP sing 303 n n C1' H1' THP sing 304 n n N1 C2 THP sing 305 n n N1 C6 THP sing 306 n n C2 O2 THP doub 307 n n C2 N3 THP sing 308 n n N3 C4 THP sing 309 n n N3 H3 THP sing 310 n n C4 O4 THP doub 311 n n C4 C5 THP sing 312 n n C5 C5M THP sing 313 n n C5 C6 THP doub 314 n n C5M H51 THP sing 315 n n C5M H52 THP sing 316 n n C5M H53 THP sing 317 n n C6 H6 THP sing 318 n n # _atom_sites.entry_id 4NMZ _atom_sites.fract_transf_matrix[1][1] 0.032185 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002494 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01655 _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] 0.026165 _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 THP A 1 201 1 THP THP . C 3 CA A 1 202 1 CA CA . D 4 HOH A 1 301 1 HOH HOH . D 4 HOH A 2 302 2 HOH HOH . D 4 HOH A 3 303 3 HOH HOH . D 4 HOH A 4 304 4 HOH HOH . D 4 HOH A 5 305 5 HOH HOH . D 4 HOH A 6 306 6 HOH HOH . D 4 HOH A 7 307 7 HOH HOH . D 4 HOH A 8 308 8 HOH HOH . D 4 HOH A 9 309 9 HOH HOH . D 4 HOH A 10 310 10 HOH HOH . D 4 HOH A 11 311 11 HOH HOH . D 4 HOH A 12 312 12 HOH HOH . D 4 HOH A 13 313 13 HOH HOH . D 4 HOH A 14 314 14 HOH HOH . D 4 HOH A 15 315 15 HOH HOH . D 4 HOH A 16 316 16 HOH HOH . D 4 HOH A 17 317 17 HOH HOH . D 4 HOH A 18 318 18 HOH HOH . D 4 HOH A 19 319 19 HOH HOH . D 4 HOH A 20 320 20 HOH HOH . D 4 HOH A 21 321 21 HOH HOH . D 4 HOH A 22 322 22 HOH HOH . D 4 HOH A 23 323 23 HOH HOH . D 4 HOH A 24 324 24 HOH HOH . D 4 HOH A 25 325 25 HOH HOH . D 4 HOH A 26 326 26 HOH HOH . D 4 HOH A 27 327 27 HOH HOH . D 4 HOH A 28 328 28 HOH HOH . D 4 HOH A 29 329 29 HOH HOH . D 4 HOH A 30 330 30 HOH HOH . D 4 HOH A 31 331 31 HOH HOH . D 4 HOH A 32 332 32 HOH HOH . D 4 HOH A 33 333 33 HOH HOH . D 4 HOH A 34 334 34 HOH HOH . D 4 HOH A 35 335 35 HOH HOH . D 4 HOH A 36 336 36 HOH HOH . D 4 HOH A 37 337 37 HOH HOH . D 4 HOH A 38 338 38 HOH HOH . D 4 HOH A 39 339 39 HOH HOH . D 4 HOH A 40 340 40 HOH HOH . D 4 HOH A 41 341 41 HOH HOH . D 4 HOH A 42 342 42 HOH HOH . D 4 HOH A 43 343 43 HOH HOH . D 4 HOH A 44 344 44 HOH HOH . D 4 HOH A 45 345 45 HOH HOH . D 4 HOH A 46 346 46 HOH HOH . D 4 HOH A 47 347 47 HOH HOH . D 4 HOH A 48 348 48 HOH HOH . D 4 HOH A 49 349 49 HOH HOH . D 4 HOH A 50 350 50 HOH HOH . D 4 HOH A 51 351 51 HOH HOH . D 4 HOH A 52 352 52 HOH HOH . D 4 HOH A 53 353 53 HOH HOH . D 4 HOH A 54 354 54 HOH HOH . D 4 HOH A 55 355 56 HOH HOH . D 4 HOH A 56 356 57 HOH HOH . D 4 HOH A 57 357 58 HOH HOH . D 4 HOH A 58 358 59 HOH HOH . D 4 HOH A 59 359 60 HOH HOH . D 4 HOH A 60 360 61 HOH HOH . D 4 HOH A 61 361 62 HOH HOH . D 4 HOH A 62 362 63 HOH HOH . D 4 HOH A 63 363 64 HOH HOH . D 4 HOH A 64 364 66 HOH HOH . D 4 HOH A 65 365 67 HOH HOH . D 4 HOH A 66 366 68 HOH HOH . D 4 HOH A 67 367 70 HOH HOH . D 4 HOH A 68 368 71 HOH HOH . D 4 HOH A 69 369 72 HOH HOH . D 4 HOH A 70 370 73 HOH HOH . D 4 HOH A 71 371 74 HOH HOH . D 4 HOH A 72 372 75 HOH HOH . D 4 HOH A 73 373 76 HOH HOH . D 4 HOH A 74 374 77 HOH HOH . D 4 HOH A 75 375 78 HOH HOH . D 4 HOH A 76 376 79 HOH HOH . D 4 HOH A 77 377 80 HOH HOH . D 4 HOH A 78 378 81 HOH HOH . D 4 HOH A 79 379 82 HOH HOH . D 4 HOH A 80 380 83 HOH HOH . D 4 HOH A 81 381 84 HOH HOH . D 4 HOH A 82 382 85 HOH HOH . D 4 HOH A 83 383 86 HOH HOH . D 4 HOH A 84 384 87 HOH HOH . D 4 HOH A 85 385 88 HOH HOH . D 4 HOH A 86 386 89 HOH HOH . D 4 HOH A 87 387 90 HOH HOH . D 4 HOH A 88 388 91 HOH HOH . D 4 HOH A 89 389 92 HOH HOH . D 4 HOH A 90 390 93 HOH HOH . D 4 HOH A 91 391 94 HOH HOH . D 4 HOH A 92 392 95 HOH HOH . D 4 HOH A 93 393 96 HOH HOH . D 4 HOH A 94 394 97 HOH HOH . D 4 HOH A 95 395 98 HOH HOH . D 4 HOH A 96 396 99 HOH HOH . D 4 HOH A 97 397 100 HOH HOH . D 4 HOH A 98 398 101 HOH HOH . D 4 HOH A 99 399 102 HOH HOH . D 4 HOH A 100 400 103 HOH HOH . D 4 HOH A 101 401 104 HOH HOH . D 4 HOH A 102 402 105 HOH HOH . D 4 HOH A 103 403 106 HOH HOH . D 4 HOH A 104 404 107 HOH HOH . D 4 HOH A 105 405 108 HOH HOH . D 4 HOH A 106 406 109 HOH HOH . D 4 HOH A 107 407 110 HOH HOH . D 4 HOH A 108 408 111 HOH HOH . D 4 HOH A 109 409 112 HOH HOH . D 4 HOH A 110 410 113 HOH HOH . D 4 HOH A 111 411 114 HOH HOH . D 4 HOH A 112 412 115 HOH HOH . D 4 HOH A 113 413 116 HOH HOH . D 4 HOH A 114 414 117 HOH HOH . D 4 HOH A 115 415 118 HOH HOH . D 4 HOH A 116 416 119 HOH HOH . D 4 HOH A 117 417 120 HOH HOH . D 4 HOH A 118 418 121 HOH HOH . D 4 HOH A 119 419 122 HOH HOH . D 4 HOH A 120 420 123 HOH HOH . D 4 HOH A 121 421 124 HOH HOH . D 4 HOH A 122 422 126 HOH HOH . D 4 HOH A 123 423 127 HOH HOH . D 4 HOH A 124 424 128 HOH HOH . D 4 HOH A 125 425 129 HOH HOH . D 4 HOH A 126 426 131 HOH HOH . D 4 HOH A 127 427 132 HOH HOH . D 4 HOH A 128 428 133 HOH HOH . D 4 HOH A 129 429 135 HOH HOH . D 4 HOH A 130 430 136 HOH HOH . D 4 HOH A 131 431 137 HOH HOH . D 4 HOH A 132 432 138 HOH HOH . D 4 HOH A 133 433 139 HOH HOH . D 4 HOH A 134 434 140 HOH HOH . D 4 HOH A 135 435 141 HOH HOH . D 4 HOH A 136 436 142 HOH HOH . D 4 HOH A 137 437 143 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 P2 THP . . . B 2 17.923 11.164 4.863 1 18.58 ? P2 THP 201 A 1 HETATM 2 O O4P THP . . . B 2 17.925 9.681 5.174 1 19.19 ? O4P THP 201 A 1 HETATM 3 O O5P THP . . . B 2 16.709 11.875 5.403 1 19.27 ? O5P THP 201 A 1 HETATM 4 O O6P THP . . . B 2 19.161 11.848 5.398 1 22.76 ? O6P THP 201 A 1 HETATM 5 P P1 THP . . . B 2 21.167 14.755 1.143 1 21.69 ? P1 THP 201 A 1 HETATM 6 O O1P THP . . . B 2 22.157 15.37 0.215 1 21.52 ? O1P THP 201 A 1 HETATM 7 O O2P THP . . . B 2 21.837 13.59 1.885 1 23.66 ? O2P THP 201 A 1 HETATM 8 O O3P THP . . . B 2 20.485 15.68 2.093 1 22.89 ? O3P THP 201 A 1 HETATM 9 O O5' THP . . . B 2 17.886 11.253 3.252 1 17.63 ? O5' THP 201 A 1 HETATM 10 C C5' THP . . . B 2 17.911 12.564 2.695 1 19.66 ? C5' THP 201 A 1 HETATM 11 C C4' THP . . . B 2 18.837 12.536 1.494 1 20.28 ? C4' THP 201 A 1 HETATM 12 O O4' THP . . . B 2 18.464 11.457 0.711 1 18.09 ? O4' THP 201 A 1 HETATM 13 C C3' THP . . . B 2 18.709 13.773 0.583 1 19.28 ? C3' THP 201 A 1 HETATM 14 O O3' THP . . . B 2 20.061 14.066 0.142 1 19.28 ? O3' THP 201 A 1 HETATM 15 C C2' THP . . . B 2 17.904 13.304 -0.574 1 17.67 ? C2' THP 201 A 1 HETATM 16 C C1' THP . . . B 2 18.221 11.798 -0.649 1 16.87 ? C1' THP 201 A 1 HETATM 17 N N1 THP . . . B 2 16.895 11.19 -1.045 1 16.07 ? N1 THP 201 A 1 HETATM 18 C C2 THP . . . B 2 16.608 10.944 -2.417 1 17.63 ? C2 THP 201 A 1 HETATM 19 O O2 THP . . . B 2 17.525 11.247 -3.213 1 17.68 ? O2 THP 201 A 1 HETATM 20 N N3 THP . . . B 2 15.447 10.393 -2.855 1 17.45 ? N3 THP 201 A 1 HETATM 21 C C4 THP . . . B 2 14.498 10.087 -1.921 1 15.86 ? C4 THP 201 A 1 HETATM 22 O O4 THP . . . B 2 13.416 9.69 -2.342 1 17.6 ? O4 THP 201 A 1 HETATM 23 C C5 THP . . . B 2 14.757 10.307 -0.498 1 15.09 ? C5 THP 201 A 1 HETATM 24 C C5M THP . . . B 2 13.652 9.94 0.434 1 17.61 ? C5M THP 201 A 1 HETATM 25 C C6 THP . . . B 2 15.99 10.859 -0.082 1 17.18 ? C6 THP 201 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #