data_4DLC # _model_server_result.job_id oCkhKj1HDJvsJzCuWldjwQ _model_server_result.datetime_utc '2024-12-01 23:43:33' _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 4dlc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4DLC # _exptl.entry_id 4DLC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _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 90 _cell.entry_id 4DLC _cell.length_a 68.28 _cell.length_b 68.28 _cell.length_c 123.66 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DLC _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 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 _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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 61.83 # _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 OE2 GLU 51 A GLU 48 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc2 A OE1 GLU 51 A GLU 48 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc3 A OE2 GLU 54 A GLU 51 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc4 A OE1 GLU 54 A GLU 51 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc5 A OE1 GLU 54 A GLU 51 1_555 F MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc6 A OE1 GLU 79 A GLU 76 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc7 A OE2 GLU 79 A GLU 76 1_555 F MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc8 A OD2 ASP 82 A ASP 79 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc9 B OP1 UMP . A UMP 301 1_555 C MG MGF . A MGF 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc10 B OP2 UMP . A UMP 301 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? metalc ? metalc11 C MG MGF . A MGF 302 1_555 G O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc12 D MG MG . A MG 303 1_555 G O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc13 D MG MG . A MG 303 1_555 G O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc14 E MG MG . A MG 304 1_555 G O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc15 F MG MG . A MG 305 1_555 G O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc16 F MG MG . A MG 305 1_555 G O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc17 F MG MG . A MG 305 1_555 G O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc18 F MG MG . A MG 305 1_555 G O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 N1 C2 UMP sing 361 n n N1 C6 UMP sing 362 n n N1 C1' UMP sing 363 n n C2 N3 UMP sing 364 n n C2 O2 UMP doub 365 n n N3 C4 UMP sing 366 n n N3 HN3 UMP sing 367 n n C4 C5 UMP sing 368 n n C4 O4 UMP doub 369 n n C5 C6 UMP doub 370 n n C5 H5 UMP sing 371 n n C6 H6 UMP sing 372 n n C1' C2' UMP sing 373 n n C1' O4' UMP sing 374 n n C1' H1' UMP sing 375 n n C2' C3' UMP sing 376 n n C2' H2' UMP sing 377 n n C2' "H2''" UMP sing 378 n n C3' C4' UMP sing 379 n n C3' O3' UMP sing 380 n n C3' H3' UMP sing 381 n n C4' O4' UMP sing 382 n n C4' C5' UMP sing 383 n n C4' H4' UMP sing 384 n n O3' HO3' UMP sing 385 n n C5' O5' UMP sing 386 n n C5' H5' UMP sing 387 n n C5' "H5''" UMP sing 388 n n O5' P UMP sing 389 n n P OP1 UMP doub 390 n n P OP2 UMP sing 391 n n P OP3 UMP sing 392 n n OP2 HOP2 UMP sing 393 n n OP3 HOP3 UMP sing 394 n n # _atom_sites.entry_id 4DLC _atom_sites.fract_transf_matrix[1][1] 0.014646 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014646 _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] 0.008087 _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 UMP A 1 301 1 UMP UMP . C 3 MGF A 1 302 2 MGF MGF . D 4 MG A 1 303 1 MG MG . E 4 MG A 1 304 2 MG MG . F 4 MG A 1 305 3 MG MG . G 5 HOH A 1 401 1 HOH HOH . G 5 HOH A 2 402 2 HOH HOH . G 5 HOH A 3 403 3 HOH HOH . G 5 HOH A 4 404 4 HOH HOH . G 5 HOH A 5 405 5 HOH HOH . G 5 HOH A 6 406 6 HOH HOH . G 5 HOH A 7 407 7 HOH HOH . G 5 HOH A 8 408 8 HOH HOH . G 5 HOH A 9 409 9 HOH HOH . G 5 HOH A 10 410 10 HOH HOH . G 5 HOH A 11 411 11 HOH HOH . G 5 HOH A 12 412 12 HOH HOH . G 5 HOH A 13 413 13 HOH HOH . G 5 HOH A 14 414 14 HOH HOH . G 5 HOH A 15 415 15 HOH HOH . G 5 HOH A 16 416 16 HOH HOH . G 5 HOH A 17 417 17 HOH HOH . G 5 HOH A 18 418 18 HOH HOH . G 5 HOH A 19 419 19 HOH HOH . G 5 HOH A 20 420 20 HOH HOH . G 5 HOH A 21 421 21 HOH HOH . G 5 HOH A 22 422 22 HOH HOH . G 5 HOH A 23 423 23 HOH HOH . G 5 HOH A 24 424 24 HOH HOH . G 5 HOH A 25 425 25 HOH HOH . G 5 HOH A 26 426 26 HOH HOH . G 5 HOH A 27 427 27 HOH HOH . G 5 HOH A 28 428 28 HOH HOH . G 5 HOH A 29 429 29 HOH HOH . G 5 HOH A 30 430 30 HOH HOH . G 5 HOH A 31 431 31 HOH HOH . G 5 HOH A 32 432 32 HOH HOH . G 5 HOH A 33 433 33 HOH HOH . G 5 HOH A 34 434 34 HOH HOH . G 5 HOH A 35 435 35 HOH HOH . G 5 HOH A 36 436 36 HOH HOH . G 5 HOH A 37 437 37 HOH HOH . G 5 HOH A 38 438 38 HOH HOH . G 5 HOH A 39 439 39 HOH HOH . G 5 HOH A 40 440 40 HOH HOH . G 5 HOH A 41 441 41 HOH HOH . G 5 HOH A 42 442 42 HOH HOH . G 5 HOH A 43 443 43 HOH HOH . G 5 HOH A 44 444 44 HOH HOH . G 5 HOH A 45 445 45 HOH HOH . G 5 HOH A 46 446 46 HOH HOH . G 5 HOH A 47 447 47 HOH HOH . G 5 HOH A 48 448 48 HOH HOH . G 5 HOH A 49 449 49 HOH HOH . G 5 HOH A 50 450 50 HOH HOH . G 5 HOH A 51 451 51 HOH HOH . G 5 HOH A 52 452 52 HOH HOH . G 5 HOH A 53 453 53 HOH HOH . G 5 HOH A 54 454 54 HOH HOH . G 5 HOH A 55 455 55 HOH HOH . G 5 HOH A 56 456 56 HOH HOH . G 5 HOH A 57 457 57 HOH HOH . G 5 HOH A 58 458 58 HOH HOH . G 5 HOH A 59 459 59 HOH HOH . G 5 HOH A 60 460 60 HOH HOH . G 5 HOH A 61 461 61 HOH HOH . G 5 HOH A 62 462 62 HOH HOH . G 5 HOH A 63 463 63 HOH HOH . G 5 HOH A 64 464 64 HOH HOH . G 5 HOH A 65 465 65 HOH HOH . G 5 HOH A 66 466 66 HOH HOH . G 5 HOH A 67 467 67 HOH HOH . G 5 HOH A 68 468 68 HOH HOH . G 5 HOH A 69 469 69 HOH HOH . G 5 HOH A 70 470 70 HOH HOH . G 5 HOH A 71 471 71 HOH HOH . G 5 HOH A 72 472 72 HOH HOH . G 5 HOH A 73 473 73 HOH HOH . G 5 HOH A 74 474 74 HOH HOH . G 5 HOH A 75 475 75 HOH HOH . G 5 HOH A 76 476 76 HOH HOH . G 5 HOH A 77 477 77 HOH HOH . G 5 HOH A 78 478 78 HOH HOH . G 5 HOH A 79 479 79 HOH HOH . G 5 HOH A 80 480 80 HOH HOH . G 5 HOH A 81 481 81 HOH HOH . G 5 HOH A 82 482 82 HOH HOH . G 5 HOH A 83 483 83 HOH HOH . G 5 HOH A 84 484 84 HOH HOH . G 5 HOH A 85 485 85 HOH HOH . G 5 HOH A 86 486 86 HOH HOH . G 5 HOH A 87 487 87 HOH HOH . G 5 HOH A 88 488 88 HOH HOH . G 5 HOH A 89 489 89 HOH HOH . G 5 HOH A 90 490 90 HOH HOH . G 5 HOH A 91 491 91 HOH HOH . G 5 HOH A 92 492 92 HOH HOH . G 5 HOH A 93 493 93 HOH HOH . G 5 HOH A 94 494 94 HOH HOH . G 5 HOH A 95 495 95 HOH HOH . G 5 HOH A 96 496 96 HOH HOH . G 5 HOH A 97 497 97 HOH HOH . G 5 HOH A 98 498 98 HOH HOH . G 5 HOH A 99 499 99 HOH HOH . G 5 HOH A 100 500 100 HOH HOH . G 5 HOH A 101 501 101 HOH HOH . G 5 HOH A 102 502 102 HOH HOH . G 5 HOH A 103 503 103 HOH HOH . G 5 HOH A 104 504 104 HOH HOH . G 5 HOH A 105 505 105 HOH HOH . G 5 HOH A 106 506 106 HOH HOH . G 5 HOH A 107 507 107 HOH HOH . G 5 HOH A 108 508 108 HOH HOH . G 5 HOH A 109 509 109 HOH HOH . G 5 HOH A 110 510 110 HOH HOH . G 5 HOH A 111 511 111 HOH HOH . G 5 HOH A 112 512 112 HOH HOH . G 5 HOH A 113 513 113 HOH HOH . G 5 HOH A 114 514 114 HOH HOH . G 5 HOH A 115 515 115 HOH HOH . G 5 HOH A 116 516 116 HOH HOH . G 5 HOH A 117 517 117 HOH HOH . G 5 HOH A 118 518 118 HOH HOH . G 5 HOH A 119 519 119 HOH HOH . G 5 HOH A 120 520 120 HOH HOH . G 5 HOH A 121 521 121 HOH HOH . G 5 HOH A 122 522 122 HOH HOH . G 5 HOH A 123 523 124 HOH HOH . G 5 HOH A 124 524 125 HOH HOH . G 5 HOH A 125 525 126 HOH HOH . G 5 HOH A 126 526 128 HOH HOH . G 5 HOH A 127 527 129 HOH HOH . G 5 HOH A 128 528 130 HOH HOH . G 5 HOH A 129 529 131 HOH HOH . G 5 HOH A 130 530 132 HOH HOH . G 5 HOH A 131 531 133 HOH HOH . G 5 HOH A 132 532 134 HOH HOH . G 5 HOH A 133 533 135 HOH HOH . G 5 HOH A 134 534 136 HOH HOH . G 5 HOH A 135 535 137 HOH HOH . G 5 HOH A 136 536 138 HOH HOH . G 5 HOH A 137 537 139 HOH HOH . G 5 HOH A 138 538 140 HOH HOH . G 5 HOH A 139 539 141 HOH HOH . G 5 HOH A 140 540 142 HOH HOH . G 5 HOH A 141 541 144 HOH HOH . G 5 HOH A 142 542 145 HOH HOH . G 5 HOH A 143 543 146 HOH HOH . G 5 HOH A 144 544 147 HOH HOH . G 5 HOH A 145 545 148 HOH HOH . G 5 HOH A 146 546 149 HOH HOH . G 5 HOH A 147 547 150 HOH HOH . G 5 HOH A 148 548 151 HOH HOH . G 5 HOH A 149 549 152 HOH HOH . G 5 HOH A 150 550 153 HOH HOH . G 5 HOH A 151 551 154 HOH HOH . G 5 HOH A 152 552 155 HOH HOH . G 5 HOH A 153 553 156 HOH HOH . G 5 HOH A 154 554 157 HOH HOH . G 5 HOH A 155 555 158 HOH HOH . G 5 HOH A 156 556 159 HOH HOH . G 5 HOH A 157 557 160 HOH HOH . G 5 HOH A 158 558 161 HOH HOH . G 5 HOH A 159 559 162 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 N N1 UMP . . . B 2 -1.514 19.344 20.78 1 15.12 ? N1 UMP 301 A 1 HETATM 2 C C2 UMP . . . B 2 -0.428 19.38 19.943 1 18.01 ? C2 UMP 301 A 1 HETATM 3 N N3 UMP . . . B 2 0.809 19.695 20.456 1 17.17 ? N3 UMP 301 A 1 HETATM 4 C C4 UMP . . . B 2 0.999 20.033 21.772 1 18.6 ? C4 UMP 301 A 1 HETATM 5 C C5 UMP . . . B 2 -0.119 19.996 22.61 1 15.67 ? C5 UMP 301 A 1 HETATM 6 C C6 UMP . . . B 2 -1.365 19.688 22.1 1 17.63 ? C6 UMP 301 A 1 HETATM 7 O O2 UMP . . . B 2 -0.572 19.088 18.761 1 16.56 ? O2 UMP 301 A 1 HETATM 8 O O4 UMP . . . B 2 2.148 20.324 22.198 1 15.48 ? O4 UMP 301 A 1 HETATM 9 C C1' UMP . . . B 2 -2.833 19.005 20.171 1 14.64 ? C1' UMP 301 A 1 HETATM 10 C C2' UMP . . . B 2 -2.984 17.568 19.767 1 12.15 ? C2' UMP 301 A 1 HETATM 11 C C3' UMP . . . B 2 -4.456 17.233 19.929 1 14.5 ? C3' UMP 301 A 1 HETATM 12 C C4' UMP . . . B 2 -4.97 18.41 20.724 1 18.95 ? C4' UMP 301 A 1 HETATM 13 O O3' UMP . . . B 2 -5.068 17.172 18.649 1 14.59 ? O3' UMP 301 A 1 HETATM 14 O O4' UMP . . . B 2 -3.845 19.158 21.136 1 17.72 ? O4' UMP 301 A 1 HETATM 15 C C5' UMP . . . B 2 -5.78 17.978 21.934 1 20.83 ? C5' UMP 301 A 1 HETATM 16 O O5' UMP . . . B 2 -6.218 19.141 22.616 1 26.87 ? O5' UMP 301 A 1 HETATM 17 P P UMP . . . B 2 -7.361 18.815 23.723 1 261.87 ? P UMP 301 A 1 HETATM 18 O OP1 UMP . . . B 2 -8.766 18.892 23.245 1 38.74 ? OP1 UMP 301 A 1 HETATM 19 O OP2 UMP . . . B 2 -7.123 17.569 24.526 1 41.73 ? OP2 UMP 301 A 1 HETATM 20 O OP3 UMP . . . B 2 -7.179 19.784 24.797 1 30.48 ? OP3 UMP 301 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #