data_4DL8 # _model_server_result.job_id drrmZJ1MrGKdTRz9xy4KpQ _model_server_result.datetime_utc '2024-10-19 10:21:29' _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 4dl8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4DL8 # _exptl.entry_id 4DL8 _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 4DL8 _cell.length_a 68.59 _cell.length_b 68.59 _cell.length_c 123.759 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DL8 _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,H _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 61.8795 # _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 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc2 A OE1 GLU 51 A GLU 48 1_555 F MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc3 A OE2 GLU 54 A GLU 51 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc4 A OE1 GLU 54 A GLU 51 1_555 F MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc5 A OE1 GLU 54 A GLU 51 1_555 G NA NA . A NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc6 A OE1 GLU 79 A GLU 76 1_555 F MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc7 A OE2 GLU 79 A GLU 76 1_555 G NA NA . A NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc8 A OD2 ASP 82 A ASP 79 1_555 F MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc9 B OP1 UMP . A UMP 301 1_555 C AL AF3 . A AF3 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc10 B OP2 UMP . A UMP 301 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? metalc ? metalc11 C AL AF3 . A AF3 302 1_555 D O1 PO4 . A PO4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? metalc ? metalc12 C AL AF3 . A AF3 302 1_555 H O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc13 D O2 PO4 . A PO4 303 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc14 D O1 PO4 . A PO4 303 1_555 G NA NA . A NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? metalc ? metalc15 E MG MG . A MG 304 1_555 H O HOH . A HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc16 F MG MG . A MG 305 1_555 H O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc17 G NA NA . A NA 306 1_555 H O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc18 G NA NA . A NA 306 1_555 H O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc19 G NA NA . A NA 306 1_555 H O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc20 G NA NA . A NA 306 1_555 H O HOH . A HOH 485 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.871 ? # _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 365 n n N1 C6 UMP sing 366 n n N1 C1' UMP sing 367 n n C2 N3 UMP sing 368 n n C2 O2 UMP doub 369 n n N3 C4 UMP sing 370 n n N3 HN3 UMP sing 371 n n C4 C5 UMP sing 372 n n C4 O4 UMP doub 373 n n C5 C6 UMP doub 374 n n C5 H5 UMP sing 375 n n C6 H6 UMP sing 376 n n C1' C2' UMP sing 377 n n C1' O4' UMP sing 378 n n C1' H1' UMP sing 379 n n C2' C3' UMP sing 380 n n C2' H2' UMP sing 381 n n C2' "H2''" UMP sing 382 n n C3' C4' UMP sing 383 n n C3' O3' UMP sing 384 n n C3' H3' UMP sing 385 n n C4' O4' UMP sing 386 n n C4' C5' UMP sing 387 n n C4' H4' UMP sing 388 n n O3' HO3' UMP sing 389 n n C5' O5' UMP sing 390 n n C5' H5' UMP sing 391 n n C5' "H5''" UMP sing 392 n n O5' P UMP sing 393 n n P OP1 UMP doub 394 n n P OP2 UMP sing 395 n n P OP3 UMP sing 396 n n OP2 HOP2 UMP sing 397 n n OP3 HOP3 UMP sing 398 n n # _atom_sites.entry_id 4DL8 _atom_sites.fract_transf_matrix[1][1] 0.014579 _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] 0.014579 _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] 0.00808 _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 1288 UMP UMP . C 3 AF3 A 1 302 1289 AF3 AF3 . D 4 PO4 A 1 303 1290 PO4 PO4 . E 5 MG A 1 304 1291 MG MG . F 5 MG A 1 305 1292 MG MG . G 6 NA A 1 306 1293 NA NA . H 7 HOH A 1 401 1 HOH HOH . H 7 HOH A 2 402 7 HOH HOH . H 7 HOH A 3 403 8 HOH HOH . H 7 HOH A 4 404 10 HOH HOH . H 7 HOH A 5 405 11 HOH HOH . H 7 HOH A 6 406 12 HOH HOH . H 7 HOH A 7 407 13 HOH HOH . H 7 HOH A 8 408 14 HOH HOH . H 7 HOH A 9 409 15 HOH HOH . H 7 HOH A 10 410 16 HOH HOH . H 7 HOH A 11 411 17 HOH HOH . H 7 HOH A 12 412 18 HOH HOH . H 7 HOH A 13 413 19 HOH HOH . H 7 HOH A 14 414 20 HOH HOH . H 7 HOH A 15 415 21 HOH HOH . H 7 HOH A 16 416 22 HOH HOH . H 7 HOH A 17 417 23 HOH HOH . H 7 HOH A 18 418 24 HOH HOH . H 7 HOH A 19 419 25 HOH HOH . H 7 HOH A 20 420 26 HOH HOH . H 7 HOH A 21 421 27 HOH HOH . H 7 HOH A 22 422 28 HOH HOH . H 7 HOH A 23 423 29 HOH HOH . H 7 HOH A 24 424 30 HOH HOH . H 7 HOH A 25 425 31 HOH HOH . H 7 HOH A 26 426 32 HOH HOH . H 7 HOH A 27 427 33 HOH HOH . H 7 HOH A 28 428 34 HOH HOH . H 7 HOH A 29 429 35 HOH HOH . H 7 HOH A 30 430 36 HOH HOH . H 7 HOH A 31 431 37 HOH HOH . H 7 HOH A 32 432 38 HOH HOH . H 7 HOH A 33 433 39 HOH HOH . H 7 HOH A 34 434 40 HOH HOH . H 7 HOH A 35 435 41 HOH HOH . H 7 HOH A 36 436 42 HOH HOH . H 7 HOH A 37 437 43 HOH HOH . H 7 HOH A 38 438 44 HOH HOH . H 7 HOH A 39 439 45 HOH HOH . H 7 HOH A 40 440 47 HOH HOH . H 7 HOH A 41 441 48 HOH HOH . H 7 HOH A 42 442 49 HOH HOH . H 7 HOH A 43 443 50 HOH HOH . H 7 HOH A 44 444 51 HOH HOH . H 7 HOH A 45 445 52 HOH HOH . H 7 HOH A 46 446 53 HOH HOH . H 7 HOH A 47 447 54 HOH HOH . H 7 HOH A 48 448 55 HOH HOH . H 7 HOH A 49 449 56 HOH HOH . H 7 HOH A 50 450 57 HOH HOH . H 7 HOH A 51 451 58 HOH HOH . H 7 HOH A 52 452 59 HOH HOH . H 7 HOH A 53 453 60 HOH HOH . H 7 HOH A 54 454 61 HOH HOH . H 7 HOH A 55 455 62 HOH HOH . H 7 HOH A 56 456 63 HOH HOH . H 7 HOH A 57 457 64 HOH HOH . H 7 HOH A 58 458 65 HOH HOH . H 7 HOH A 59 459 66 HOH HOH . H 7 HOH A 60 460 68 HOH HOH . H 7 HOH A 61 461 69 HOH HOH . H 7 HOH A 62 462 70 HOH HOH . H 7 HOH A 63 463 71 HOH HOH . H 7 HOH A 64 464 72 HOH HOH . H 7 HOH A 65 465 73 HOH HOH . H 7 HOH A 66 466 74 HOH HOH . H 7 HOH A 67 467 75 HOH HOH . H 7 HOH A 68 468 76 HOH HOH . H 7 HOH A 69 469 77 HOH HOH . H 7 HOH A 70 470 78 HOH HOH . H 7 HOH A 71 471 79 HOH HOH . H 7 HOH A 72 472 80 HOH HOH . H 7 HOH A 73 473 81 HOH HOH . H 7 HOH A 74 474 82 HOH HOH . H 7 HOH A 75 475 83 HOH HOH . H 7 HOH A 76 476 84 HOH HOH . H 7 HOH A 77 477 85 HOH HOH . H 7 HOH A 78 478 86 HOH HOH . H 7 HOH A 79 479 87 HOH HOH . H 7 HOH A 80 480 89 HOH HOH . H 7 HOH A 81 481 90 HOH HOH . H 7 HOH A 82 482 91 HOH HOH . H 7 HOH A 83 483 94 HOH HOH . H 7 HOH A 84 484 95 HOH HOH . H 7 HOH A 85 485 96 HOH HOH . H 7 HOH A 86 486 97 HOH HOH . H 7 HOH A 87 487 98 HOH HOH . H 7 HOH A 88 488 100 HOH HOH . H 7 HOH A 89 489 101 HOH HOH . H 7 HOH A 90 490 102 HOH HOH . H 7 HOH A 91 491 103 HOH HOH . H 7 HOH A 92 492 105 HOH HOH . H 7 HOH A 93 493 106 HOH HOH . H 7 HOH A 94 494 107 HOH HOH . H 7 HOH A 95 495 108 HOH HOH . H 7 HOH A 96 496 109 HOH HOH . H 7 HOH A 97 497 112 HOH HOH . H 7 HOH A 98 498 113 HOH HOH . H 7 HOH A 99 499 115 HOH HOH . H 7 HOH A 100 500 116 HOH HOH . H 7 HOH A 101 501 118 HOH HOH . H 7 HOH A 102 502 119 HOH HOH . H 7 HOH A 103 503 120 HOH HOH . H 7 HOH A 104 504 121 HOH HOH . H 7 HOH A 105 505 122 HOH HOH . H 7 HOH A 106 506 123 HOH HOH . H 7 HOH A 107 507 124 HOH HOH . H 7 HOH A 108 508 125 HOH HOH . H 7 HOH A 109 509 126 HOH HOH . H 7 HOH A 110 510 127 HOH HOH . H 7 HOH A 111 511 128 HOH HOH . H 7 HOH A 112 512 129 HOH HOH . H 7 HOH A 113 513 130 HOH HOH . H 7 HOH A 114 514 131 HOH HOH . H 7 HOH A 115 515 132 HOH HOH . H 7 HOH A 116 516 133 HOH HOH . H 7 HOH A 117 517 134 HOH HOH . H 7 HOH A 118 518 135 HOH HOH . H 7 HOH A 119 519 136 HOH HOH . H 7 HOH A 120 520 137 HOH HOH . H 7 HOH A 121 521 138 HOH HOH . H 7 HOH A 122 522 139 HOH HOH . H 7 HOH A 123 523 140 HOH HOH . H 7 HOH A 124 524 141 HOH HOH . H 7 HOH A 125 525 142 HOH HOH . H 7 HOH A 126 526 143 HOH HOH . H 7 HOH A 127 527 144 HOH HOH . H 7 HOH A 128 528 145 HOH HOH . H 7 HOH A 129 529 146 HOH HOH . H 7 HOH A 130 530 147 HOH HOH . H 7 HOH A 131 531 148 HOH HOH . H 7 HOH A 132 532 149 HOH HOH . H 7 HOH A 133 533 150 HOH HOH . H 7 HOH A 134 534 151 HOH HOH . H 7 HOH A 135 535 152 HOH HOH . H 7 HOH A 136 536 153 HOH HOH . H 7 HOH A 137 537 154 HOH HOH . H 7 HOH A 138 538 155 HOH HOH . H 7 HOH A 139 539 156 HOH HOH . H 7 HOH A 140 540 157 HOH HOH . H 7 HOH A 141 541 158 HOH HOH . H 7 HOH A 142 542 159 HOH HOH . H 7 HOH A 143 543 160 HOH HOH . H 7 HOH A 144 544 161 HOH HOH . H 7 HOH A 145 545 162 HOH HOH . H 7 HOH A 146 546 163 HOH HOH . H 7 HOH A 147 547 164 HOH HOH . H 7 HOH A 148 548 165 HOH HOH . H 7 HOH A 149 549 166 HOH HOH . H 7 HOH A 150 550 167 HOH HOH . H 7 HOH A 151 551 168 HOH HOH . H 7 HOH A 152 552 169 HOH HOH . H 7 HOH A 153 553 170 HOH HOH . H 7 HOH A 154 554 171 HOH HOH . H 7 HOH A 155 555 172 HOH HOH . H 7 HOH A 156 556 173 HOH HOH . H 7 HOH A 157 557 174 HOH HOH . H 7 HOH A 158 558 175 HOH HOH . H 7 HOH A 159 559 176 HOH HOH . H 7 HOH A 160 560 177 HOH HOH . H 7 HOH A 161 561 178 HOH HOH . H 7 HOH A 162 562 179 HOH HOH . H 7 HOH A 163 563 180 HOH HOH . H 7 HOH A 164 564 181 HOH HOH . H 7 HOH A 165 565 182 HOH HOH . H 7 HOH A 166 566 183 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 -1.618 19.313 20.863 1 17.55 ? N1 UMP 301 A 1 HETATM 2 C C2 UMP . . . B 2 -0.525 19.334 20.033 1 19.26 ? C2 UMP 301 A 1 HETATM 3 N N3 UMP . . . B 2 0.707 19.674 20.541 1 16.48 ? N3 UMP 301 A 1 HETATM 4 C C4 UMP . . . B 2 0.908 20.024 21.845 1 21.63 ? C4 UMP 301 A 1 HETATM 5 C C5 UMP . . . B 2 -0.218 20.023 22.674 1 15.9 ? C5 UMP 301 A 1 HETATM 6 C C6 UMP . . . B 2 -1.462 19.696 22.175 1 15.86 ? C6 UMP 301 A 1 HETATM 7 O O2 UMP . . . B 2 -0.671 19.059 18.854 1 16.07 ? O2 UMP 301 A 1 HETATM 8 O O4 UMP . . . B 2 2.06 20.315 22.244 1 18.96 ? O4 UMP 301 A 1 HETATM 9 C C1' UMP . . . B 2 -2.942 18.982 20.309 1 16.41 ? C1' UMP 301 A 1 HETATM 10 C C2' UMP . . . B 2 -3.084 17.591 19.781 1 13.92 ? C2' UMP 301 A 1 HETATM 11 C C3' UMP . . . B 2 -4.561 17.228 19.937 1 14.64 ? C3' UMP 301 A 1 HETATM 12 C C4' UMP . . . B 2 -5.072 18.356 20.828 1 14.35 ? C4' UMP 301 A 1 HETATM 13 O O3' UMP . . . B 2 -5.237 17.19 18.686 1 12.49 ? O3' UMP 301 A 1 HETATM 14 O O4' UMP . . . B 2 -3.935 19.079 21.313 1 14.06 ? O4' UMP 301 A 1 HETATM 15 C C5' UMP . . . B 2 -5.876 17.855 22.035 1 15.7 ? C5' UMP 301 A 1 HETATM 16 O O5' UMP . . . B 2 -6.313 18.986 22.755 1 16.42 ? O5' UMP 301 A 1 HETATM 17 P P UMP . . . B 2 -7.304 18.796 24.053 1 17.46 ? P UMP 301 A 1 HETATM 18 O OP1 UMP . . . B 2 -8.733 18.769 23.582 1 16.14 ? OP1 UMP 301 A 1 HETATM 19 O OP2 UMP . . . B 2 -6.939 17.512 24.719 1 17.42 ? OP2 UMP 301 A 1 HETATM 20 O OP3 UMP . . . B 2 -7.104 20.024 24.893 1 17.76 ? OP3 UMP 301 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 20 #