data_5CCY # _model_server_result.job_id gV5i3pgUGmvg4ylPmSW-gg _model_server_result.datetime_utc '2024-11-24 01:56:43' _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 5ccy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 5CCY # _exptl.entry_id 5CCY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-PHOSPHATE" _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 5CCY _cell.length_a 73.908 _cell.length_b 73.908 _cell.length_c 128.282 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CCY _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64 2 2' # _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,E _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 3 _struct_asym.id D _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 NE2 HIS 41 A HIS 41 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc2 A OE2 GLU 61 A GLU 80 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc3 A OD2 ASP 89 A ASP 108 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc4 A OD1 ASP 89 A ASP 108 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc5 A OE2 GLU 100 A GLU 119 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc6 A O ILE 101 A ILE 120 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc7 B MN MN . A MN 301 1_555 D O2P TMP . A TMP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc8 B MN MN . A MN 301 1_555 D O1P TMP . A TMP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc9 C MN MN . A MN 302 1_555 D O2P TMP . A TMP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc10 C MN MN . A MN 302 1_555 E O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc11 C MN MN . A MN 302 1_555 E O HOH . A HOH 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc12 C MN MN . A MN 302 1_555 E O HOH . A HOH 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-PHOSPHATE" _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 P O1P TMP doub 306 n n P O2P TMP sing 307 n n P O3P TMP sing 308 n n P O5' TMP sing 309 n n O2P HOP2 TMP sing 310 n n O3P HOP3 TMP sing 311 n n O5' C5' TMP sing 312 n n C5' C4' TMP sing 313 n n C5' "H5'1" TMP sing 314 n n C5' "H5'2" TMP sing 315 n n C4' O4' TMP sing 316 n n C4' C3' TMP sing 317 n n C4' H4' TMP sing 318 n n O4' C1' TMP sing 319 n n C3' O3' TMP sing 320 n n C3' C2' TMP sing 321 n n C3' H3' TMP sing 322 n n O3' HO3' TMP sing 323 n n C2' C1' TMP sing 324 n n C2' "H2'1" TMP sing 325 n n C2' "H2'2" TMP sing 326 n n C1' N1 TMP sing 327 n n C1' H1' TMP sing 328 n n N1 C2 TMP sing 329 n n N1 C6 TMP sing 330 n n C2 O2 TMP doub 331 n n C2 N3 TMP sing 332 n n N3 C4 TMP sing 333 n n N3 HN3 TMP sing 334 n n C4 O4 TMP doub 335 n n C4 C5 TMP sing 336 n n C5 C5M TMP sing 337 n n C5 C6 TMP doub 338 n n C5M H51 TMP sing 339 n n C5M H52 TMP sing 340 n n C5M H53 TMP sing 341 n n C6 H6 TMP sing 342 n n # _atom_sites.entry_id 5CCY _atom_sites.fract_transf_matrix[1][1] 0.01353 _atom_sites.fract_transf_matrix[1][2] 0.007812 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015623 _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] 0.007795 _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 MN A 1 301 201 MN MN . C 2 MN A 1 302 202 MN MN . D 3 TMP A 1 303 203 TMP TMP . E 4 HOH A 1 401 330 HOH HOH . E 4 HOH A 2 402 388 HOH HOH . E 4 HOH A 3 403 324 HOH HOH . E 4 HOH A 4 404 303 HOH HOH . E 4 HOH A 5 405 382 HOH HOH . E 4 HOH A 6 406 312 HOH HOH . E 4 HOH A 7 407 387 HOH HOH . E 4 HOH A 8 408 345 HOH HOH . E 4 HOH A 9 409 351 HOH HOH . E 4 HOH A 10 410 367 HOH HOH . E 4 HOH A 11 411 316 HOH HOH . E 4 HOH A 12 412 360 HOH HOH . E 4 HOH A 13 413 346 HOH HOH . E 4 HOH A 14 414 364 HOH HOH . E 4 HOH A 15 415 368 HOH HOH . E 4 HOH A 16 416 358 HOH HOH . E 4 HOH A 17 417 327 HOH HOH . E 4 HOH A 18 418 334 HOH HOH . E 4 HOH A 19 419 317 HOH HOH . E 4 HOH A 20 420 313 HOH HOH . E 4 HOH A 21 421 338 HOH HOH . E 4 HOH A 22 422 350 HOH HOH . E 4 HOH A 23 423 333 HOH HOH . E 4 HOH A 24 424 306 HOH HOH . E 4 HOH A 25 425 335 HOH HOH . E 4 HOH A 26 426 314 HOH HOH . E 4 HOH A 27 427 354 HOH HOH . E 4 HOH A 28 428 329 HOH HOH . E 4 HOH A 29 429 376 HOH HOH . E 4 HOH A 30 430 373 HOH HOH . E 4 HOH A 31 431 304 HOH HOH . E 4 HOH A 32 432 323 HOH HOH . E 4 HOH A 33 433 309 HOH HOH . E 4 HOH A 34 434 307 HOH HOH . E 4 HOH A 35 435 384 HOH HOH . E 4 HOH A 36 436 319 HOH HOH . E 4 HOH A 37 437 352 HOH HOH . E 4 HOH A 38 438 321 HOH HOH . E 4 HOH A 39 439 348 HOH HOH . E 4 HOH A 40 440 344 HOH HOH . E 4 HOH A 41 441 337 HOH HOH . E 4 HOH A 42 442 308 HOH HOH . E 4 HOH A 43 443 318 HOH HOH . E 4 HOH A 44 444 362 HOH HOH . E 4 HOH A 45 445 302 HOH HOH . E 4 HOH A 46 446 355 HOH HOH . E 4 HOH A 47 447 363 HOH HOH . E 4 HOH A 48 448 315 HOH HOH . E 4 HOH A 49 449 341 HOH HOH . E 4 HOH A 50 450 311 HOH HOH . E 4 HOH A 51 451 322 HOH HOH . E 4 HOH A 52 452 359 HOH HOH . E 4 HOH A 53 453 325 HOH HOH . E 4 HOH A 54 454 349 HOH HOH . E 4 HOH A 55 455 381 HOH HOH . E 4 HOH A 56 456 357 HOH HOH . E 4 HOH A 57 457 356 HOH HOH . E 4 HOH A 58 458 383 HOH HOH . E 4 HOH A 59 459 371 HOH HOH . E 4 HOH A 60 460 353 HOH HOH . E 4 HOH A 61 461 328 HOH HOH . E 4 HOH A 62 462 305 HOH HOH . E 4 HOH A 63 463 332 HOH HOH . E 4 HOH A 64 464 386 HOH HOH . E 4 HOH A 65 465 378 HOH HOH . E 4 HOH A 66 466 320 HOH HOH . E 4 HOH A 67 467 369 HOH HOH . E 4 HOH A 68 468 380 HOH HOH . E 4 HOH A 69 469 347 HOH HOH . E 4 HOH A 70 470 365 HOH HOH . E 4 HOH A 71 471 339 HOH HOH . E 4 HOH A 72 472 310 HOH HOH . E 4 HOH A 73 473 301 HOH HOH . E 4 HOH A 74 474 377 HOH HOH . E 4 HOH A 75 475 326 HOH HOH . E 4 HOH A 76 476 374 HOH HOH . E 4 HOH A 77 477 340 HOH HOH . E 4 HOH A 78 478 379 HOH HOH . E 4 HOH A 79 479 366 HOH HOH . E 4 HOH A 80 480 361 HOH HOH . E 4 HOH A 81 481 342 HOH HOH . E 4 HOH A 82 482 331 HOH HOH . E 4 HOH A 83 483 375 HOH HOH . E 4 HOH A 84 484 336 HOH HOH . E 4 HOH A 85 485 385 HOH HOH . E 4 HOH A 86 486 343 HOH HOH . E 4 HOH A 87 487 370 HOH HOH . E 4 HOH A 88 488 372 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 P TMP . . . D 3 -9.796 78.039 16.592 1 30.15 ? P TMP 303 A 1 HETATM 2 O O1P TMP . . . D 3 -9.775 76.691 15.756 1 26.79 ? O1P TMP 303 A 1 HETATM 3 O O2P TMP . . . D 3 -11.136 78.024 17.294 1 25.86 ? O2P TMP 303 A 1 HETATM 4 O O3P TMP . . . D 3 -8.497 78.372 17.377 1 28.65 ? O3P TMP 303 A 1 HETATM 5 O O5' TMP . . . D 3 -9.796 79.205 15.481 1 29.61 ? O5' TMP 303 A 1 HETATM 6 C C5' TMP . . . D 3 -10.901 79.368 14.632 1 33.84 ? C5' TMP 303 A 1 HETATM 7 C C4' TMP . . . D 3 -10.594 80.09 13.345 1 31.17 ? C4' TMP 303 A 1 HETATM 8 O O4' TMP . . . D 3 -10.217 81.387 13.719 1 32.73 ? O4' TMP 303 A 1 HETATM 9 C C3' TMP . . . D 3 -9.375 79.532 12.567 1 34.91 ? C3' TMP 303 A 1 HETATM 10 O O3' TMP . . . D 3 -9.735 79.657 11.19 1 35.89 ? O3' TMP 303 A 1 HETATM 11 C C2' TMP . . . D 3 -8.146 80.4 12.896 1 34.75 ? C2' TMP 303 A 1 HETATM 12 C C1' TMP . . . D 3 -8.884 81.708 13.256 1 37.18 ? C1' TMP 303 A 1 HETATM 13 N N1 TMP . . . D 3 -8.188 82.505 14.277 1 37.94 ? N1 TMP 303 A 1 HETATM 14 C C2 TMP . . . D 3 -7.415 83.658 13.868 1 38.94 ? C2 TMP 303 A 1 HETATM 15 O O2 TMP . . . D 3 -7.315 84.043 12.657 1 37.88 ? O2 TMP 303 A 1 HETATM 16 N N3 TMP . . . D 3 -6.808 84.347 14.822 1 36.65 ? N3 TMP 303 A 1 HETATM 17 C C4 TMP . . . D 3 -6.869 83.976 16.087 1 39.45 ? C4 TMP 303 A 1 HETATM 18 O O4 TMP . . . D 3 -6.301 84.603 16.931 1 42.84 ? O4 TMP 303 A 1 HETATM 19 C C5 TMP . . . D 3 -7.616 82.807 16.54 1 37.89 ? C5 TMP 303 A 1 HETATM 20 C C5M TMP . . . D 3 -7.674 82.415 17.987 1 39.18 ? C5M TMP 303 A 1 HETATM 21 C C6 TMP . . . D 3 -8.252 82.11 15.547 1 36.47 ? C6 TMP 303 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 21 #