data_6LHI
#
_model_server_result.job_id            kWtAoDL7pDYDfCDZpgEmoA 
_model_server_result.datetime_utc      '2024-11-15 16:46:21' 
_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          6lhi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":801}' 
#
_entry.id    6LHI 
#
_exptl.entry_id    6LHI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          3 
_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         90 
_cell.entry_id            6LHI 
_cell.length_a            56.308 
_cell.length_b            154.488 
_cell.length_c            163.939 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6LHI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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,I,J,K 
_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
? 3 D N N 
? 3 G 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 498 n n 
N1 C6 UMP sing 499 n n 
N1 C1' UMP sing 500 n n 
C2 N3 UMP sing 501 n n 
C2 O2 UMP doub 502 n n 
N3 C4 UMP sing 503 n n 
N3 HN3 UMP sing 504 n n 
C4 C5 UMP sing 505 n n 
C4 O4 UMP doub 506 n n 
C5 C6 UMP doub 507 n n 
C5 H5 UMP sing 508 n n 
C6 H6 UMP sing 509 n n 
C1' C2' UMP sing 510 n n 
C1' O4' UMP sing 511 n n 
C1' H1' UMP sing 512 n n 
C2' C3' UMP sing 513 n n 
C2' H2' UMP sing 514 n n 
C2' "H2''" UMP sing 515 n n 
C3' C4' UMP sing 516 n n 
C3' O3' UMP sing 517 n n 
C3' H3' UMP sing 518 n n 
C4' O4' UMP sing 519 n n 
C4' C5' UMP sing 520 n n 
C4' H4' UMP sing 521 n n 
O3' HO3' UMP sing 522 n n 
C5' O5' UMP sing 523 n n 
C5' H5' UMP sing 524 n n 
C5' "H5''" UMP sing 525 n n 
O5' P UMP sing 526 n n 
P OP1 UMP doub 527 n n 
P OP2 UMP sing 528 n n 
P OP3 UMP sing 529 n n 
OP2 HOP2 UMP sing 530 n n 
OP3 HOP3 UMP sing 531 n n 
#
_atom_sites.entry_id                     6LHI 
_atom_sites.fract_transf_matrix[1][1]    0.017759 
_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]    0.006473 
_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]    0.0061 
_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 MET A 1 701 606 MET MET . 
D 3 UMP A 1 702 801 UMP UMP . 
E 4 E9X A 1 703 901 E9X DRG . 
F 5 NDP A 1 704 1001 NDP NDP . 
G 3 UMP B 1 801 801 UMP UMP . 
H 4 E9X B 1 802 901 E9X DRG . 
I 5 NDP B 1 803 1001 NDP NDP . 
J 6 HOH A 1 801 65 HOH HOH . 
J 6 HOH A 2 802 71 HOH HOH . 
J 6 HOH A 3 803 28 HOH HOH . 
J 6 HOH A 4 804 91 HOH HOH . 
J 6 HOH A 5 805 57 HOH HOH . 
J 6 HOH A 6 806 17 HOH HOH . 
J 6 HOH A 7 807 92 HOH HOH . 
J 6 HOH A 8 808 24 HOH HOH . 
J 6 HOH A 9 809 63 HOH HOH . 
J 6 HOH A 10 810 32 HOH HOH . 
J 6 HOH A 11 811 70 HOH HOH . 
J 6 HOH A 12 812 38 HOH HOH . 
J 6 HOH A 13 813 23 HOH HOH . 
J 6 HOH A 14 814 8 HOH HOH . 
J 6 HOH A 15 815 22 HOH HOH . 
J 6 HOH A 16 816 80 HOH HOH . 
J 6 HOH A 17 817 2 HOH HOH . 
J 6 HOH A 18 818 88 HOH HOH . 
J 6 HOH A 19 819 93 HOH HOH . 
J 6 HOH A 20 820 25 HOH HOH . 
J 6 HOH A 21 821 50 HOH HOH . 
J 6 HOH A 22 822 89 HOH HOH . 
J 6 HOH A 23 823 12 HOH HOH . 
J 6 HOH A 24 824 68 HOH HOH . 
J 6 HOH A 25 825 59 HOH HOH . 
J 6 HOH A 26 826 90 HOH HOH . 
J 6 HOH A 27 827 7 HOH HOH . 
J 6 HOH A 28 828 31 HOH HOH . 
J 6 HOH A 29 829 5 HOH HOH . 
J 6 HOH A 30 830 61 HOH HOH . 
J 6 HOH A 31 831 3 HOH HOH . 
J 6 HOH A 32 832 66 HOH HOH . 
J 6 HOH A 33 833 94 HOH HOH . 
J 6 HOH A 34 834 78 HOH HOH . 
J 6 HOH A 35 835 64 HOH HOH . 
J 6 HOH A 36 836 87 HOH HOH . 
J 6 HOH A 37 837 49 HOH HOH . 
J 6 HOH A 38 838 11 HOH HOH . 
J 6 HOH A 39 839 16 HOH HOH . 
J 6 HOH A 40 840 52 HOH HOH . 
J 6 HOH A 41 841 79 HOH HOH . 
J 6 HOH A 42 842 54 HOH HOH . 
J 6 HOH A 43 843 47 HOH HOH . 
J 6 HOH A 44 844 19 HOH HOH . 
J 6 HOH A 45 845 15 HOH HOH . 
J 6 HOH A 46 846 10 HOH HOH . 
J 6 HOH A 47 847 67 HOH HOH . 
K 6 HOH B 1 901 39 HOH HOH . 
K 6 HOH B 2 902 34 HOH HOH . 
K 6 HOH B 3 903 42 HOH HOH . 
K 6 HOH B 4 904 44 HOH HOH . 
K 6 HOH B 5 905 1 HOH HOH . 
K 6 HOH B 6 906 58 HOH HOH . 
K 6 HOH B 7 907 75 HOH HOH . 
K 6 HOH B 8 908 76 HOH HOH . 
K 6 HOH B 9 909 20 HOH HOH . 
K 6 HOH B 10 910 18 HOH HOH . 
K 6 HOH B 11 911 96 HOH HOH . 
K 6 HOH B 12 912 48 HOH HOH . 
K 6 HOH B 13 913 83 HOH HOH . 
K 6 HOH B 14 914 74 HOH HOH . 
K 6 HOH B 15 915 84 HOH HOH . 
K 6 HOH B 16 916 9 HOH HOH . 
K 6 HOH B 17 917 46 HOH HOH . 
K 6 HOH B 18 918 35 HOH HOH . 
K 6 HOH B 19 919 69 HOH HOH . 
K 6 HOH B 20 920 43 HOH HOH . 
K 6 HOH B 21 921 13 HOH HOH . 
K 6 HOH B 22 922 4 HOH HOH . 
K 6 HOH B 23 923 72 HOH HOH . 
K 6 HOH B 24 924 40 HOH HOH . 
K 6 HOH B 25 925 95 HOH HOH . 
K 6 HOH B 26 926 6 HOH HOH . 
K 6 HOH B 27 927 41 HOH HOH . 
K 6 HOH B 28 928 81 HOH HOH . 
K 6 HOH B 29 929 14 HOH HOH . 
K 6 HOH B 30 930 29 HOH HOH . 
K 6 HOH B 31 931 86 HOH HOH . 
K 6 HOH B 32 932 56 HOH HOH . 
K 6 HOH B 33 933 82 HOH HOH . 
K 6 HOH B 34 934 53 HOH HOH . 
K 6 HOH B 35 935 73 HOH HOH . 
K 6 HOH B 36 936 21 HOH HOH . 
K 6 HOH B 37 937 55 HOH HOH . 
K 6 HOH B 38 938 77 HOH HOH . 
K 6 HOH B 39 939 30 HOH HOH . 
K 6 HOH B 40 940 62 HOH HOH . 
K 6 HOH B 41 941 36 HOH HOH . 
K 6 HOH B 42 942 51 HOH HOH . 
K 6 HOH B 43 943 37 HOH HOH . 
K 6 HOH B 44 944 26 HOH HOH . 
K 6 HOH B 45 945 27 HOH HOH . 
K 6 HOH B 46 946 45 HOH HOH . 
K 6 HOH B 47 947 60 HOH HOH . 
K 6 HOH B 48 948 33 HOH HOH . 
K 6 HOH B 49 949 85 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 . . . G 3 12.662 -13.701 9.151 1 42.24 ? N1 UMP 801 B 1 
HETATM 2 C C2 UMP . . . G 3 11.782 -12.622 9.177 1 40.7 ? C2 UMP 801 B 1 
HETATM 3 N N3 UMP . . . G 3 10.927 -12.55 8.112 1 42.14 ? N3 UMP 801 B 1 
HETATM 4 C C4 UMP . . . G 3 10.842 -13.423 7.043 1 45.74 ? C4 UMP 801 B 1 
HETATM 5 C C5 UMP . . . G 3 11.796 -14.501 7.078 1 46.21 ? C5 UMP 801 B 1 
HETATM 6 C C6 UMP . . . G 3 12.668 -14.582 8.094 1 43.24 ? C6 UMP 801 B 1 
HETATM 7 O O2 UMP . . . G 3 11.714 -11.793 10.074 1 37.13 ? O2 UMP 801 B 1 
HETATM 8 O O4 UMP . . . G 3 9.997 -13.217 6.165 1 41.25 ? O4 UMP 801 B 1 
HETATM 9 C C1' UMP . . . G 3 13.695 -13.827 10.204 1 44.13 ? C1' UMP 801 B 1 
HETATM 10 C C2' UMP . . . G 3 13.251 -14.368 11.547 1 48.73 ? C2' UMP 801 B 1 
HETATM 11 C C3' UMP . . . G 3 14.517 -15.08 12.021 1 47.5 ? C3' UMP 801 B 1 
HETATM 12 C C4' UMP . . . G 3 14.878 -15.79 10.731 1 45.73 ? C4' UMP 801 B 1 
HETATM 13 O O3' UMP . . . G 3 15.569 -14.187 12.403 1 39.24 ? O3' UMP 801 B 1 
HETATM 14 O O4' UMP . . . G 3 14.666 -14.759 9.739 1 51.81 ? O4' UMP 801 B 1 
HETATM 15 C C5' UMP . . . G 3 14.056 -17.017 10.399 1 45.17 ? C5' UMP 801 B 1 
HETATM 16 O O5' UMP . . . G 3 14.709 -18.212 10.927 1 39.52 ? O5' UMP 801 B 1 
HETATM 17 P P UMP . . . G 3 13.926 -19.164 11.932 1 34.78 ? P UMP 801 B 1 
HETATM 18 O OP1 UMP . . . G 3 14.994 -19.935 12.657 1 36.45 ? OP1 UMP 801 B 1 
HETATM 19 O OP2 UMP . . . G 3 13.162 -18.206 12.812 1 32.88 ? OP2 UMP 801 B 1 
HETATM 20 O OP3 UMP . . . G 3 13.036 -20.07 11.136 1 30.35 ? OP3 UMP 801 B 1 
HETATM 21 H HN3 UMP . . . G 3 10.355 -11.87 8.128 1 42.14 ? HN3 UMP 801 B 1 
HETATM 22 H H5 UMP . . . G 3 11.83 -15.118 6.376 1 46.21 ? H5 UMP 801 B 1 
HETATM 23 H H6 UMP . . . G 3 13.331 -15.245 8.068 1 43.24 ? H6 UMP 801 B 1 
HETATM 24 H H1' UMP . . . G 3 14.117 -12.932 10.312 1 44.13 ? H1' UMP 801 B 1 
HETATM 25 H H2' UMP . . . G 3 12.987 -13.659 12.17 1 48.73 ? H2' UMP 801 B 1 
HETATM 26 H "H2''" UMP . . . G 3 12.499 -14.992 11.472 1 48.73 ? "H2''" UMP 801 B 1 
HETATM 27 H H3' UMP . . . G 3 14.327 -15.647 12.81 1 47.5 ? H3' UMP 801 B 1 
HETATM 28 H H4' UMP . . . G 3 15.832 -16.043 10.717 1 45.73 ? H4' UMP 801 B 1 
HETATM 29 H HO3' UMP . . . G 3 16.192 -14.231 11.828 0 39.24 ? HO3' UMP 801 B 1 
HETATM 30 H H5' UMP . . . G 3 13.966 -17.105 9.417 1 45.17 ? H5' UMP 801 B 1 
HETATM 31 H "H5''" UMP . . . G 3 13.155 -16.937 10.801 1 45.17 ? "H5''" UMP 801 B 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          22 
_model_server_stats.element_count           31 
#