data_1I00 # _model_server_result.job_id AVkB55pQutm0TJ5xmQU9vg _model_server_result.datetime_utc '2025-02-17 09:16:09' _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 1i00 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":408}' # _entry.id 1I00 # _exptl.entry_id 1I00 _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 2 _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 1I00 _cell.length_a 89.689 _cell.length_b 89.689 _cell.length_c 142.129 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1I00 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _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 # _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N # _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 414 n n N1 C6 UMP sing 415 n n N1 C1' UMP sing 416 n n C2 N3 UMP sing 417 n n C2 O2 UMP doub 418 n n N3 C4 UMP sing 419 n n N3 HN3 UMP sing 420 n n C4 C5 UMP sing 421 n n C4 O4 UMP doub 422 n n C5 C6 UMP doub 423 n n C5 H5 UMP sing 424 n n C6 H6 UMP sing 425 n n C1' C2' UMP sing 426 n n C1' O4' UMP sing 427 n n C1' H1' UMP sing 428 n n C2' C3' UMP sing 429 n n C2' H2' UMP sing 430 n n C2' "H2''" UMP sing 431 n n C3' C4' UMP sing 432 n n C3' O3' UMP sing 433 n n C3' H3' UMP sing 434 n n C4' O4' UMP sing 435 n n C4' C5' UMP sing 436 n n C4' H4' UMP sing 437 n n O3' HO3' UMP sing 438 n n C5' O5' UMP sing 439 n n C5' H5' UMP sing 440 n n C5' "H5''" UMP sing 441 n n O5' P UMP sing 442 n n P OP1 UMP doub 443 n n P OP2 UMP sing 444 n n P OP3 UMP sing 445 n n OP2 HOP2 UMP sing 446 n n OP3 HOP3 UMP sing 447 n n # _atom_sites.entry_id 1I00 _atom_sites.fract_transf_matrix[1][1] 0.01115 _atom_sites.fract_transf_matrix[1][2] 0.006437 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012874 _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] 0.007036 _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 C 2 UMP A 1 314 308 UMP UMP . D 3 D16 A 1 315 309 D16 D16 . E 2 UMP B 1 408 408 UMP UMP . F 3 D16 B 1 409 409 D16 D16 . G 4 HOH A 1 502 502 HOH WAT . G 4 HOH A 2 503 503 HOH WAT . G 4 HOH A 3 504 504 HOH WAT . G 4 HOH A 4 505 505 HOH WAT . G 4 HOH A 5 507 507 HOH WAT . G 4 HOH A 6 509 509 HOH WAT . G 4 HOH A 7 510 510 HOH WAT . G 4 HOH A 8 511 511 HOH WAT . G 4 HOH A 9 512 512 HOH WAT . G 4 HOH A 10 515 515 HOH WAT . G 4 HOH A 11 516 516 HOH WAT . G 4 HOH A 12 517 517 HOH WAT . G 4 HOH A 13 518 518 HOH WAT . G 4 HOH A 14 520 520 HOH WAT . G 4 HOH A 15 521 521 HOH WAT . G 4 HOH A 16 523 523 HOH WAT . G 4 HOH A 17 524 524 HOH WAT . G 4 HOH A 18 525 525 HOH WAT . G 4 HOH A 19 527 527 HOH WAT . G 4 HOH A 20 528 528 HOH WAT . G 4 HOH A 21 529 529 HOH WAT . G 4 HOH A 22 532 532 HOH WAT . G 4 HOH A 23 533 533 HOH WAT . G 4 HOH A 24 534 534 HOH WAT . G 4 HOH A 25 538 538 HOH WAT . G 4 HOH A 26 539 539 HOH WAT . G 4 HOH A 27 543 543 HOH WAT . G 4 HOH A 28 547 547 HOH WAT . G 4 HOH A 29 548 548 HOH WAT . G 4 HOH A 30 549 549 HOH WAT . G 4 HOH A 31 550 550 HOH WAT . G 4 HOH A 32 553 553 HOH WAT . G 4 HOH A 33 555 555 HOH WAT . G 4 HOH A 34 557 557 HOH WAT . G 4 HOH A 35 560 560 HOH WAT . G 4 HOH A 36 561 561 HOH WAT . G 4 HOH A 37 563 563 HOH WAT . G 4 HOH A 38 564 564 HOH WAT . G 4 HOH A 39 567 567 HOH WAT . G 4 HOH A 40 568 568 HOH WAT . G 4 HOH A 41 570 570 HOH WAT . G 4 HOH A 42 571 571 HOH WAT . G 4 HOH A 43 572 572 HOH WAT . G 4 HOH A 44 573 573 HOH WAT . G 4 HOH A 45 574 574 HOH WAT . G 4 HOH A 46 575 575 HOH WAT . G 4 HOH A 47 576 576 HOH WAT . G 4 HOH A 48 578 578 HOH WAT . G 4 HOH A 49 579 579 HOH WAT . G 4 HOH A 50 580 580 HOH WAT . G 4 HOH A 51 581 581 HOH WAT . G 4 HOH A 52 584 584 HOH WAT . G 4 HOH A 53 585 585 HOH WAT . G 4 HOH A 54 586 586 HOH WAT . G 4 HOH A 55 587 587 HOH WAT . G 4 HOH A 56 588 588 HOH WAT . G 4 HOH A 57 591 591 HOH WAT . G 4 HOH A 58 592 592 HOH WAT . G 4 HOH A 59 593 593 HOH WAT . G 4 HOH A 60 595 595 HOH WAT . G 4 HOH A 61 596 596 HOH WAT . G 4 HOH A 62 599 599 HOH WAT . G 4 HOH A 63 603 603 HOH WAT . G 4 HOH A 64 604 604 HOH WAT . G 4 HOH A 65 605 605 HOH WAT . G 4 HOH A 66 606 606 HOH WAT . G 4 HOH A 67 607 607 HOH WAT . G 4 HOH A 68 608 608 HOH WAT . G 4 HOH A 69 609 609 HOH WAT . H 4 HOH B 1 501 501 HOH WAT . H 4 HOH B 2 506 506 HOH WAT . H 4 HOH B 3 508 508 HOH WAT . H 4 HOH B 4 513 513 HOH WAT . H 4 HOH B 5 514 514 HOH WAT . H 4 HOH B 6 519 519 HOH WAT . H 4 HOH B 7 522 522 HOH WAT . H 4 HOH B 8 526 526 HOH WAT . H 4 HOH B 9 530 530 HOH WAT . H 4 HOH B 10 531 531 HOH WAT . H 4 HOH B 11 535 535 HOH WAT . H 4 HOH B 12 536 536 HOH WAT . H 4 HOH B 13 537 537 HOH WAT . H 4 HOH B 14 540 540 HOH WAT . H 4 HOH B 15 541 541 HOH WAT . H 4 HOH B 16 542 542 HOH WAT . H 4 HOH B 17 544 544 HOH WAT . H 4 HOH B 18 545 545 HOH WAT . H 4 HOH B 19 546 546 HOH WAT . H 4 HOH B 20 551 551 HOH WAT . H 4 HOH B 21 552 552 HOH WAT . H 4 HOH B 22 554 554 HOH WAT . H 4 HOH B 23 556 556 HOH WAT . H 4 HOH B 24 558 558 HOH WAT . H 4 HOH B 25 559 559 HOH WAT . H 4 HOH B 26 562 562 HOH WAT . H 4 HOH B 27 565 565 HOH WAT . H 4 HOH B 28 566 566 HOH WAT . H 4 HOH B 29 569 569 HOH WAT . H 4 HOH B 30 577 577 HOH WAT . H 4 HOH B 31 582 582 HOH WAT . H 4 HOH B 32 583 583 HOH WAT . H 4 HOH B 33 589 589 HOH WAT . H 4 HOH B 34 590 590 HOH WAT . H 4 HOH B 35 594 594 HOH WAT . H 4 HOH B 36 597 597 HOH WAT . H 4 HOH B 37 598 598 HOH WAT . H 4 HOH B 38 600 600 HOH WAT . H 4 HOH B 39 601 601 HOH WAT . H 4 HOH B 40 602 602 HOH WAT . H 4 HOH B 41 610 610 HOH WAT . # 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 . . . E 2 14.609 38.499 28.774 1 59.71 ? N1 UMP 408 B 1 HETATM 2 C C2 UMP . . . E 2 15.63 37.717 29.388 1 60.54 ? C2 UMP 408 B 1 HETATM 3 N N3 UMP . . . E 2 16.877 37.79 28.741 1 60.62 ? N3 UMP 408 B 1 HETATM 4 C C4 UMP . . . E 2 17.203 38.542 27.579 1 62.2 ? C4 UMP 408 B 1 HETATM 5 C C5 UMP . . . E 2 16.117 39.312 27.014 1 60.87 ? C5 UMP 408 B 1 HETATM 6 C C6 UMP . . . E 2 14.905 39.267 27.606 1 60.5 ? C6 UMP 408 B 1 HETATM 7 O O2 UMP . . . E 2 15.464 37.03 30.39 1 61.87 ? O2 UMP 408 B 1 HETATM 8 O O4 UMP . . . E 2 18.354 38.504 27.121 1 62.31 ? O4 UMP 408 B 1 HETATM 9 C C1' UMP . . . E 2 13.208 38.511 29.365 1 59.46 ? C1' UMP 408 B 1 HETATM 10 C C2' UMP . . . E 2 13.051 38.93 30.718 1 59.26 ? C2' UMP 408 B 1 HETATM 11 C C3' UMP . . . E 2 11.706 39.444 30.751 1 58.93 ? C3' UMP 408 B 1 HETATM 12 C C4' UMP . . . E 2 11.455 39.997 29.434 1 57.97 ? C4' UMP 408 B 1 HETATM 13 O O3' UMP . . . E 2 10.834 38.324 31.042 1 57.33 ? O3' UMP 408 B 1 HETATM 14 O O4' UMP . . . E 2 12.405 39.349 28.597 1 58.87 ? O4' UMP 408 B 1 HETATM 15 C C5' UMP . . . E 2 11.841 41.43 29.278 1 55.79 ? C5' UMP 408 B 1 HETATM 16 O O5' UMP . . . E 2 10.843 42.333 28.916 1 51.56 ? O5' UMP 408 B 1 HETATM 17 P P UMP . . . E 2 10.676 43.707 29.742 1 49.92 ? P UMP 408 B 1 HETATM 18 O OP1 UMP . . . E 2 10.967 44.735 28.703 1 51.31 ? OP1 UMP 408 B 1 HETATM 19 O OP2 UMP . . . E 2 9.254 43.734 30.26 1 51.05 ? OP2 UMP 408 B 1 HETATM 20 O OP3 UMP . . . E 2 11.692 43.72 30.862 1 51.15 ? OP3 UMP 408 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #