data_1JTU
#
_model_server_result.job_id            7eZcOPs4Iy-1SstfpVBy7w 
_model_server_result.datetime_utc      '2024-12-03 17:55:19' 
_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          1jtu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":565}' 
#
_entry.id    1JTU 
#
_exptl.entry_id    1JTU 
_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            1JTU 
_cell.length_a            127.6 
_cell.length_b            127.6 
_cell.length_c            68 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1JTU 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale2 A SG CYS 146 A CYS 146 1_555 C C6 UMP . A UMP 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? 
covale ? covale3 B C CXM 1 B CXM 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 B SG CYS 146 B CYS 146 1_555 E C6 UMP . B UMP 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.843 ? 
#
_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 482 n n 
N1 C6 UMP sing 483 n n 
N1 C1' UMP sing 484 n n 
C2 N3 UMP sing 485 n n 
C2 O2 UMP doub 486 n n 
N3 C4 UMP sing 487 n n 
N3 HN3 UMP sing 488 n n 
C4 C5 UMP sing 489 n n 
C4 O4 UMP doub 490 n n 
C5 C6 UMP doub 491 n n 
C5 H5 UMP sing 492 n n 
C6 H6 UMP sing 493 n n 
C1' C2' UMP sing 494 n n 
C1' O4' UMP sing 495 n n 
C1' H1' UMP sing 496 n n 
C2' C3' UMP sing 497 n n 
C2' H2' UMP sing 498 n n 
C2' "H2''" UMP sing 499 n n 
C3' C4' UMP sing 500 n n 
C3' O3' UMP sing 501 n n 
C3' H3' UMP sing 502 n n 
C4' O4' UMP sing 503 n n 
C4' C5' UMP sing 504 n n 
C4' H4' UMP sing 505 n n 
O3' HO3' UMP sing 506 n n 
C5' O5' UMP sing 507 n n 
C5' H5' UMP sing 508 n n 
C5' "H5''" UMP sing 509 n n 
O5' P UMP sing 510 n n 
P OP1 UMP doub 511 n n 
P OP2 UMP sing 512 n n 
P OP3 UMP sing 513 n n 
OP2 HOP2 UMP sing 514 n n 
OP3 HOP3 UMP sing 515 n n 
#
_atom_sites.entry_id                     1JTU 
_atom_sites.fract_transf_matrix[1][1]    0.007837 
_atom_sites.fract_transf_matrix[1][2]    0.004525 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009049 
_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]    0.014706 
_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 LYB A 1 501 566 LYB LYB . 
E 2 UMP B 1 565 565 UMP DUM . 
F 3 LYB B 1 502 566 LYB LYB . 
G 4 HOH A 1 637 637 HOH WAT . 
G 4 HOH A 2 638 638 HOH WAT . 
G 4 HOH A 3 640 640 HOH WAT . 
G 4 HOH A 4 641 641 HOH WAT . 
G 4 HOH A 5 642 642 HOH WAT . 
G 4 HOH A 6 643 643 HOH WAT . 
G 4 HOH A 7 644 644 HOH WAT . 
G 4 HOH A 8 646 646 HOH WAT . 
G 4 HOH A 9 647 647 HOH WAT . 
G 4 HOH A 10 649 649 HOH WAT . 
G 4 HOH A 11 650 650 HOH WAT . 
G 4 HOH A 12 652 652 HOH WAT . 
G 4 HOH A 13 653 653 HOH WAT . 
G 4 HOH A 14 655 655 HOH WAT . 
G 4 HOH A 15 656 656 HOH WAT . 
G 4 HOH A 16 659 659 HOH WAT . 
G 4 HOH A 17 660 660 HOH WAT . 
G 4 HOH A 18 662 662 HOH WAT . 
G 4 HOH A 19 664 664 HOH WAT . 
G 4 HOH A 20 665 665 HOH WAT . 
G 4 HOH A 21 668 668 HOH WAT . 
G 4 HOH A 22 670 670 HOH WAT . 
G 4 HOH A 23 671 671 HOH WAT . 
G 4 HOH A 24 677 677 HOH WAT . 
G 4 HOH A 25 679 679 HOH WAT . 
G 4 HOH A 26 680 680 HOH WAT . 
G 4 HOH A 27 682 682 HOH WAT . 
G 4 HOH A 28 684 684 HOH WAT . 
G 4 HOH A 29 685 685 HOH WAT . 
G 4 HOH A 30 688 688 HOH WAT . 
G 4 HOH A 31 689 689 HOH WAT . 
G 4 HOH A 32 690 690 HOH WAT . 
G 4 HOH A 33 691 691 HOH WAT . 
G 4 HOH A 34 692 692 HOH WAT . 
G 4 HOH A 35 693 693 HOH WAT . 
G 4 HOH A 36 694 694 HOH WAT . 
G 4 HOH A 37 698 698 HOH WAT . 
G 4 HOH A 38 699 699 HOH WAT . 
G 4 HOH A 39 703 703 HOH WAT . 
G 4 HOH A 40 705 705 HOH WAT . 
G 4 HOH A 41 706 706 HOH WAT . 
G 4 HOH A 42 707 707 HOH WAT . 
G 4 HOH A 43 708 708 HOH WAT . 
G 4 HOH A 44 711 711 HOH WAT . 
G 4 HOH A 45 713 713 HOH WAT . 
G 4 HOH A 46 715 715 HOH WAT . 
G 4 HOH A 47 716 716 HOH WAT . 
G 4 HOH A 48 717 717 HOH WAT . 
G 4 HOH A 49 718 718 HOH WAT . 
G 4 HOH A 50 719 719 HOH WAT . 
G 4 HOH A 51 720 720 HOH WAT . 
G 4 HOH A 52 722 722 HOH WAT . 
G 4 HOH A 53 723 723 HOH WAT . 
G 4 HOH A 54 726 726 HOH WAT . 
G 4 HOH A 55 727 727 HOH WAT . 
G 4 HOH A 56 728 728 HOH WAT . 
G 4 HOH A 57 732 732 HOH WAT . 
G 4 HOH A 58 733 733 HOH WAT . 
G 4 HOH A 59 734 734 HOH WAT . 
G 4 HOH A 60 735 735 HOH WAT . 
G 4 HOH A 61 738 738 HOH WAT . 
G 4 HOH A 62 739 739 HOH WAT . 
G 4 HOH A 63 740 740 HOH WAT . 
G 4 HOH A 64 742 742 HOH WAT . 
G 4 HOH A 65 743 743 HOH WAT . 
G 4 HOH A 66 744 744 HOH WAT . 
G 4 HOH A 67 748 748 HOH WAT . 
G 4 HOH A 68 750 750 HOH WAT . 
G 4 HOH A 69 751 751 HOH WAT . 
G 4 HOH A 70 752 752 HOH WAT . 
G 4 HOH A 71 755 755 HOH WAT . 
G 4 HOH A 72 756 756 HOH WAT . 
G 4 HOH A 73 757 757 HOH WAT . 
G 4 HOH A 74 758 758 HOH WAT . 
G 4 HOH A 75 759 759 HOH WAT . 
G 4 HOH A 76 760 760 HOH WAT . 
G 4 HOH A 77 762 762 HOH WAT . 
G 4 HOH A 78 763 763 HOH WAT . 
G 4 HOH A 79 764 764 HOH WAT . 
G 4 HOH A 80 765 765 HOH WAT . 
G 4 HOH A 81 770 770 HOH WAT . 
G 4 HOH A 82 771 771 HOH WAT . 
G 4 HOH A 83 772 772 HOH WAT . 
G 4 HOH A 84 776 776 HOH WAT . 
G 4 HOH A 85 778 778 HOH WAT . 
G 4 HOH A 86 780 780 HOH WAT . 
G 4 HOH A 87 781 781 HOH WAT . 
G 4 HOH A 88 783 783 HOH WAT . 
G 4 HOH A 89 786 786 HOH WAT . 
G 4 HOH A 90 788 788 HOH WAT . 
G 4 HOH A 91 789 789 HOH WAT . 
G 4 HOH A 92 791 791 HOH WAT . 
G 4 HOH A 93 792 792 HOH WAT . 
G 4 HOH A 94 794 794 HOH WAT . 
G 4 HOH A 95 795 795 HOH WAT . 
G 4 HOH A 96 796 796 HOH WAT . 
G 4 HOH A 97 798 798 HOH WAT . 
G 4 HOH A 98 799 799 HOH WAT . 
G 4 HOH A 99 802 802 HOH WAT . 
G 4 HOH A 100 803 803 HOH WAT . 
G 4 HOH A 101 807 807 HOH WAT . 
G 4 HOH A 102 811 811 HOH WAT . 
G 4 HOH A 103 812 812 HOH WAT . 
G 4 HOH A 104 819 819 HOH WAT . 
G 4 HOH A 105 820 820 HOH WAT . 
G 4 HOH A 106 821 821 HOH WAT . 
G 4 HOH A 107 822 822 HOH WAT . 
G 4 HOH A 108 824 824 HOH WAT . 
G 4 HOH A 109 825 825 HOH WAT . 
G 4 HOH A 110 826 826 HOH WAT . 
G 4 HOH A 111 828 828 HOH WAT . 
G 4 HOH A 112 830 830 HOH WAT . 
H 4 HOH B 1 635 635 HOH WAT . 
H 4 HOH B 2 636 636 HOH WAT . 
H 4 HOH B 3 639 639 HOH WAT . 
H 4 HOH B 4 645 645 HOH WAT . 
H 4 HOH B 5 648 648 HOH WAT . 
H 4 HOH B 6 651 651 HOH WAT . 
H 4 HOH B 7 654 654 HOH WAT . 
H 4 HOH B 8 657 657 HOH WAT . 
H 4 HOH B 9 658 658 HOH WAT . 
H 4 HOH B 10 661 661 HOH WAT . 
H 4 HOH B 11 663 663 HOH WAT . 
H 4 HOH B 12 666 666 HOH WAT . 
H 4 HOH B 13 667 667 HOH WAT . 
H 4 HOH B 14 669 669 HOH WAT . 
H 4 HOH B 15 672 672 HOH WAT . 
H 4 HOH B 16 673 673 HOH WAT . 
H 4 HOH B 17 674 674 HOH WAT . 
H 4 HOH B 18 675 675 HOH WAT . 
H 4 HOH B 19 676 676 HOH WAT . 
H 4 HOH B 20 678 678 HOH WAT . 
H 4 HOH B 21 681 681 HOH WAT . 
H 4 HOH B 22 683 683 HOH WAT . 
H 4 HOH B 23 686 686 HOH WAT . 
H 4 HOH B 24 687 687 HOH WAT . 
H 4 HOH B 25 695 695 HOH WAT . 
H 4 HOH B 26 696 696 HOH WAT . 
H 4 HOH B 27 697 697 HOH WAT . 
H 4 HOH B 28 700 700 HOH WAT . 
H 4 HOH B 29 701 701 HOH WAT . 
H 4 HOH B 30 702 702 HOH WAT . 
H 4 HOH B 31 704 704 HOH WAT . 
H 4 HOH B 32 709 709 HOH WAT . 
H 4 HOH B 33 710 710 HOH WAT . 
H 4 HOH B 34 712 712 HOH WAT . 
H 4 HOH B 35 714 714 HOH WAT . 
H 4 HOH B 36 721 721 HOH WAT . 
H 4 HOH B 37 724 724 HOH WAT . 
H 4 HOH B 38 725 725 HOH WAT . 
H 4 HOH B 39 729 729 HOH WAT . 
H 4 HOH B 40 730 730 HOH WAT . 
H 4 HOH B 41 731 731 HOH WAT . 
H 4 HOH B 42 736 736 HOH WAT . 
H 4 HOH B 43 737 737 HOH WAT . 
H 4 HOH B 44 741 741 HOH WAT . 
H 4 HOH B 45 745 745 HOH WAT . 
H 4 HOH B 46 746 746 HOH WAT . 
H 4 HOH B 47 747 747 HOH WAT . 
H 4 HOH B 48 749 749 HOH WAT . 
H 4 HOH B 49 753 753 HOH WAT . 
H 4 HOH B 50 754 754 HOH WAT . 
H 4 HOH B 51 761 761 HOH WAT . 
H 4 HOH B 52 766 766 HOH WAT . 
H 4 HOH B 53 767 767 HOH WAT . 
H 4 HOH B 54 768 768 HOH WAT . 
H 4 HOH B 55 769 769 HOH WAT . 
H 4 HOH B 56 773 773 HOH WAT . 
H 4 HOH B 57 774 774 HOH WAT . 
H 4 HOH B 58 775 775 HOH WAT . 
H 4 HOH B 59 777 777 HOH WAT . 
H 4 HOH B 60 779 779 HOH WAT . 
H 4 HOH B 61 782 782 HOH WAT . 
H 4 HOH B 62 784 784 HOH WAT . 
H 4 HOH B 63 785 785 HOH WAT . 
H 4 HOH B 64 787 787 HOH WAT . 
H 4 HOH B 65 790 790 HOH WAT . 
H 4 HOH B 66 793 793 HOH WAT . 
H 4 HOH B 67 797 797 HOH WAT . 
H 4 HOH B 68 800 800 HOH WAT . 
H 4 HOH B 69 801 801 HOH WAT . 
H 4 HOH B 70 804 804 HOH WAT . 
H 4 HOH B 71 805 805 HOH WAT . 
H 4 HOH B 72 806 806 HOH WAT . 
H 4 HOH B 73 808 808 HOH WAT . 
H 4 HOH B 74 809 809 HOH WAT . 
H 4 HOH B 75 810 810 HOH WAT . 
H 4 HOH B 76 813 813 HOH WAT . 
H 4 HOH B 77 814 814 HOH WAT . 
H 4 HOH B 78 815 815 HOH WAT . 
H 4 HOH B 79 816 816 HOH WAT . 
H 4 HOH B 80 817 817 HOH WAT . 
H 4 HOH B 81 818 818 HOH WAT . 
H 4 HOH B 82 823 823 HOH WAT . 
H 4 HOH B 83 827 827 HOH WAT . 
H 4 HOH B 84 829 829 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 17.914 20.311 31.209 1 32.96 ? N1 UMP 565 A 1 
HETATM 2 C C2 UMP . . . C 2 18.672 20.208 32.368 1 32.54 ? C2 UMP 565 A 1 
HETATM 3 N N3 UMP . . . C 2 19.517 19.118 32.42 1 33.49 ? N3 UMP 565 A 1 
HETATM 4 C C4 UMP . . . C 2 19.809 18.255 31.38 1 33.79 ? C4 UMP 565 A 1 
HETATM 5 C C5 UMP . . . C 2 19.102 18.372 30.036 1 32.69 ? C5 UMP 565 A 1 
HETATM 6 C C6 UMP . . . C 2 18.233 19.642 29.912 1 32.08 ? C6 UMP 565 A 1 
HETATM 7 O O2 UMP . . . C 2 18.596 21.033 33.287 1 30.68 ? O2 UMP 565 A 1 
HETATM 8 O O4 UMP . . . C 2 20.658 17.381 31.566 1 33.29 ? O4 UMP 565 A 1 
HETATM 9 C C1' UMP . . . C 2 16.697 21.167 31.2 1 32.39 ? C1' UMP 565 A 1 
HETATM 10 C C2' UMP . . . C 2 16.963 22.622 30.795 1 32.97 ? C2' UMP 565 A 1 
HETATM 11 C C3' UMP . . . C 2 15.583 23.073 30.345 1 32.82 ? C3' UMP 565 A 1 
HETATM 12 C C4' UMP . . . C 2 15.032 21.91 29.505 1 32.35 ? C4' UMP 565 A 1 
HETATM 13 O O3' UMP . . . C 2 14.772 23.212 31.545 1 33.71 ? O3' UMP 565 A 1 
HETATM 14 O O4' UMP . . . C 2 15.626 20.731 30.228 1 31.41 ? O4' UMP 565 A 1 
HETATM 15 C C5' UMP . . . C 2 15.589 21.953 28.084 1 31.01 ? C5' UMP 565 A 1 
HETATM 16 O O5' UMP . . . C 2 14.859 23.036 27.461 1 30.33 ? O5' UMP 565 A 1 
HETATM 17 P P UMP . . . C 2 15.453 24.003 26.414 1 29.99 ? P UMP 565 A 1 
HETATM 18 O OP1 UMP . . . C 2 14.377 24.796 25.768 1 28.8 ? OP1 UMP 565 A 1 
HETATM 19 O OP2 UMP . . . C 2 16.357 24.905 27.166 1 28.96 ? OP2 UMP 565 A 1 
HETATM 20 O OP3 UMP . . . C 2 16.174 23.193 25.43 1 28.09 ? OP3 UMP 565 A 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#