data_1JTQ # _model_server_result.job_id v7ZjNngOfFfVTu6AWklV-w _model_server_result.datetime_utc '2024-11-27 01:10:55' _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 1jtq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":565}' # _entry.id 1JTQ # _exptl.entry_id 1JTQ _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 1JTQ _cell.length_a 127.8 _cell.length_b 127.8 _cell.length_c 68.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JTQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _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 # 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 covale ? covale1 A C CXM 1 A CXM 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale2 A SG CYS 146 A CYS 146 1_555 C C6 UMP . A UMP 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.843 ? covale ? covale3 B C CXM 1 B CXM 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale4 B SG CYS 146 B CYS 146 1_555 E C6 UMP . B UMP 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? # _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 437 n n N1 C6 UMP sing 438 n n N1 C1' UMP sing 439 n n C2 N3 UMP sing 440 n n C2 O2 UMP doub 441 n n N3 C4 UMP sing 442 n n N3 HN3 UMP sing 443 n n C4 C5 UMP sing 444 n n C4 O4 UMP doub 445 n n C5 C6 UMP doub 446 n n C5 H5 UMP sing 447 n n C6 H6 UMP sing 448 n n C1' C2' UMP sing 449 n n C1' O4' UMP sing 450 n n C1' H1' UMP sing 451 n n C2' C3' UMP sing 452 n n C2' H2' UMP sing 453 n n C2' "H2''" UMP sing 454 n n C3' C4' UMP sing 455 n n C3' O3' UMP sing 456 n n C3' H3' UMP sing 457 n n C4' O4' UMP sing 458 n n C4' C5' UMP sing 459 n n C4' H4' UMP sing 460 n n O3' HO3' UMP sing 461 n n C5' O5' UMP sing 462 n n C5' H5' UMP sing 463 n n C5' "H5''" UMP sing 464 n n O5' P UMP sing 465 n n P OP1 UMP doub 466 n n P OP2 UMP sing 467 n n P OP3 UMP sing 468 n n OP2 HOP2 UMP sing 469 n n OP3 HOP3 UMP sing 470 n n # _atom_sites.entry_id 1JTQ _atom_sites.fract_transf_matrix[1][1] 0.007825 _atom_sites.fract_transf_matrix[1][2] 0.004518 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009035 _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] 0.014684 _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 1 565 565 UMP DUM . D 3 LY3 A 1 501 566 LY3 L34 . E 2 UMP B 1 565 565 UMP DUM . F 3 LY3 B 1 502 566 LY3 L34 . G 4 HOH A 1 601 601 HOH WAT . G 4 HOH A 2 602 602 HOH WAT . G 4 HOH A 3 603 603 HOH WAT . G 4 HOH A 4 604 604 HOH WAT . G 4 HOH A 5 606 606 HOH WAT . G 4 HOH A 6 608 608 HOH WAT . G 4 HOH A 7 610 610 HOH WAT . G 4 HOH A 8 612 612 HOH WAT . G 4 HOH A 9 613 613 HOH WAT . G 4 HOH A 10 614 614 HOH WAT . G 4 HOH A 11 617 617 HOH WAT . G 4 HOH A 12 618 618 HOH WAT . G 4 HOH A 13 619 619 HOH WAT . G 4 HOH A 14 621 621 HOH WAT . G 4 HOH A 15 622 622 HOH WAT . G 4 HOH A 16 623 623 HOH WAT . G 4 HOH A 17 625 625 HOH WAT . G 4 HOH A 18 628 628 HOH WAT . G 4 HOH A 19 631 631 HOH WAT . G 4 HOH A 20 632 632 HOH WAT . G 4 HOH A 21 633 633 HOH WAT . G 4 HOH A 22 634 634 HOH WAT . G 4 HOH A 23 635 635 HOH WAT . G 4 HOH A 24 636 636 HOH WAT . G 4 HOH A 25 637 637 HOH WAT . G 4 HOH A 26 640 640 HOH WAT . G 4 HOH A 27 641 641 HOH WAT . G 4 HOH A 28 642 642 HOH WAT . G 4 HOH A 29 643 643 HOH WAT . G 4 HOH A 30 644 644 HOH WAT . G 4 HOH A 31 646 646 HOH WAT . G 4 HOH A 32 647 647 HOH WAT . G 4 HOH A 33 649 649 HOH WAT . G 4 HOH A 34 650 650 HOH WAT . G 4 HOH A 35 653 653 HOH WAT . G 4 HOH A 36 655 655 HOH WAT . G 4 HOH A 37 658 658 HOH WAT . G 4 HOH A 38 660 660 HOH WAT . G 4 HOH A 39 661 661 HOH WAT . G 4 HOH A 40 663 663 HOH WAT . G 4 HOH A 41 664 664 HOH WAT . G 4 HOH A 42 665 665 HOH WAT . G 4 HOH A 43 669 669 HOH WAT . G 4 HOH A 44 670 670 HOH WAT . G 4 HOH A 45 672 672 HOH WAT . G 4 HOH A 46 674 674 HOH WAT . G 4 HOH A 47 676 676 HOH WAT . G 4 HOH A 48 678 678 HOH WAT . G 4 HOH A 49 679 679 HOH WAT . G 4 HOH A 50 680 680 HOH WAT . G 4 HOH A 51 682 682 HOH WAT . G 4 HOH A 52 686 686 HOH WAT . G 4 HOH A 53 687 687 HOH WAT . G 4 HOH A 54 688 688 HOH WAT . G 4 HOH A 55 689 689 HOH WAT . G 4 HOH A 56 690 690 HOH WAT . G 4 HOH A 57 691 691 HOH WAT . G 4 HOH A 58 693 693 HOH WAT . G 4 HOH A 59 694 694 HOH WAT . G 4 HOH A 60 695 695 HOH WAT . G 4 HOH A 61 696 696 HOH WAT . G 4 HOH A 62 698 698 HOH WAT . G 4 HOH A 63 699 699 HOH WAT . G 4 HOH A 64 700 700 HOH WAT . G 4 HOH A 65 701 701 HOH WAT . H 4 HOH B 1 605 605 HOH WAT . H 4 HOH B 2 607 607 HOH WAT . H 4 HOH B 3 609 609 HOH WAT . H 4 HOH B 4 611 611 HOH WAT . H 4 HOH B 5 615 615 HOH WAT . H 4 HOH B 6 616 616 HOH WAT . H 4 HOH B 7 620 620 HOH WAT . H 4 HOH B 8 624 624 HOH WAT . H 4 HOH B 9 626 626 HOH WAT . H 4 HOH B 10 627 627 HOH WAT . H 4 HOH B 11 629 629 HOH WAT . H 4 HOH B 12 630 630 HOH WAT . H 4 HOH B 13 638 638 HOH WAT . H 4 HOH B 14 639 639 HOH WAT . H 4 HOH B 15 645 645 HOH WAT . H 4 HOH B 16 648 648 HOH WAT . H 4 HOH B 17 651 651 HOH WAT . H 4 HOH B 18 652 652 HOH WAT . H 4 HOH B 19 654 654 HOH WAT . H 4 HOH B 20 656 656 HOH WAT . H 4 HOH B 21 657 657 HOH WAT . H 4 HOH B 22 659 659 HOH WAT . H 4 HOH B 23 662 662 HOH WAT . H 4 HOH B 24 666 666 HOH WAT . H 4 HOH B 25 667 667 HOH WAT . H 4 HOH B 26 668 668 HOH WAT . H 4 HOH B 27 671 671 HOH WAT . H 4 HOH B 28 673 673 HOH WAT . H 4 HOH B 29 675 675 HOH WAT . H 4 HOH B 30 677 677 HOH WAT . H 4 HOH B 31 681 681 HOH WAT . H 4 HOH B 32 683 683 HOH WAT . H 4 HOH B 33 684 684 HOH WAT . H 4 HOH B 34 685 685 HOH WAT . H 4 HOH B 35 692 692 HOH WAT . H 4 HOH B 36 697 697 HOH WAT . H 4 HOH B 37 702 702 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 . . . C 2 17.83 20.311 31.142 1 39.31 ? N1 UMP 565 A 1 HETATM 2 C C2 UMP . . . C 2 18.618 20.148 32.29 1 42.17 ? C2 UMP 565 A 1 HETATM 3 N N3 UMP . . . C 2 19.465 19.064 32.296 1 41.76 ? N3 UMP 565 A 1 HETATM 4 C C4 UMP . . . C 2 19.711 18.217 31.23 1 42.58 ? C4 UMP 565 A 1 HETATM 5 C C5 UMP . . . C 2 18.891 18.334 29.948 1 39.94 ? C5 UMP 565 A 1 HETATM 6 C C6 UMP . . . C 2 18.156 19.68 29.82 1 35.6 ? C6 UMP 565 A 1 HETATM 7 O O2 UMP . . . C 2 18.585 20.924 33.249 1 46.95 ? O2 UMP 565 A 1 HETATM 8 O O4 UMP . . . C 2 20.596 17.367 31.336 1 43.79 ? O4 UMP 565 A 1 HETATM 9 C C1' UMP . . . C 2 16.611 21.159 31.18 1 36.03 ? C1' UMP 565 A 1 HETATM 10 C C2' UMP . . . C 2 16.866 22.61 30.763 1 35.28 ? C2' UMP 565 A 1 HETATM 11 C C3' UMP . . . C 2 15.479 23.051 30.326 1 34.58 ? C3' UMP 565 A 1 HETATM 12 C C4' UMP . . . C 2 14.906 21.879 29.505 1 30.21 ? C4' UMP 565 A 1 HETATM 13 O O3' UMP . . . C 2 14.736 23.264 31.551 1 29.45 ? O3' UMP 565 A 1 HETATM 14 O O4' UMP . . . C 2 15.56 20.766 30.206 1 32.6 ? O4' UMP 565 A 1 HETATM 15 C C5' UMP . . . C 2 15.464 21.855 28.084 1 28.03 ? C5' UMP 565 A 1 HETATM 16 O O5' UMP . . . C 2 14.751 22.871 27.33 1 29.88 ? O5' UMP 565 A 1 HETATM 17 P P UMP . . . C 2 15.381 24.025 26.471 1 24.57 ? P UMP 565 A 1 HETATM 18 O OP1 UMP . . . C 2 14.296 24.792 25.824 1 22.27 ? OP1 UMP 565 A 1 HETATM 19 O OP2 UMP . . . C 2 16.18 24.938 27.321 1 25.94 ? OP2 UMP 565 A 1 HETATM 20 O OP3 UMP . . . C 2 16.222 23.394 25.481 1 23.4 ? OP3 UMP 565 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 20 #