data_1OGK
#
_model_server_result.job_id            twq9o_O3xGus3F51CgWs6A 
_model_server_result.datetime_utc      '2024-11-15 03:05:06' 
_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          1ogk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1281}' 
#
_entry.id    1OGK 
#
_exptl.entry_id    1OGK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              388.162 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "DEOXYURIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          101.35 
_cell.angle_gamma         90 
_cell.entry_id            1OGK 
_cell.length_a            106.386 
_cell.length_b            50.307 
_cell.length_c            111.387 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1OGK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E 1 1 
C,D,F,G 2 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 E N N 
? 2 F N N 
? 2 G N N 
#
_chem_comp.formula           'C9 H14 N2 O11 P2' 
_chem_comp.formula_weight    388.162 
_chem_comp.id                DUD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "DEOXYURIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 DUD sing 83 n n 
N1 C6 DUD sing 84 n n 
N1 C1' DUD sing 85 n n 
C2 N3 DUD sing 86 n n 
C2 O2 DUD doub 87 n n 
N3 C4 DUD sing 88 n n 
N3 HN3 DUD sing 89 n n 
C4 C5 DUD sing 90 n n 
C4 O4 DUD doub 91 n n 
C5 C6 DUD doub 92 n n 
C5 H5 DUD sing 93 n n 
C6 H6 DUD sing 94 n n 
C1' C2' DUD sing 95 n n 
C1' O4' DUD sing 96 n n 
C1' H1' DUD sing 97 n n 
C2' C3' DUD sing 98 n n 
C2' "H2'1" DUD sing 99 n n 
C2' "H2'2" DUD sing 100 n n 
C3' C4' DUD sing 101 n n 
C3' O3' DUD sing 102 n n 
C3' H3' DUD sing 103 n n 
C4' O4' DUD sing 104 n n 
C4' C5' DUD sing 105 n n 
C4' H4' DUD sing 106 n n 
O3' HO3' DUD sing 107 n n 
C5' O5' DUD sing 108 n n 
C5' "H5'1" DUD sing 109 n n 
C5' "H5'2" DUD sing 110 n n 
O5' PA DUD sing 111 n n 
PA O1A DUD doub 112 n n 
PA O2A DUD sing 113 n n 
PA O3A DUD sing 114 n n 
O2A HOA2 DUD sing 115 n n 
O3A PB DUD sing 116 n n 
PB O1B DUD doub 117 n n 
PB O2B DUD sing 118 n n 
PB O3B DUD sing 119 n n 
O2B HOB2 DUD sing 120 n n 
O3B HOB3 DUD sing 121 n n 
#
_atom_sites.entry_id                     1OGK 
_atom_sites.fract_transf_matrix[1][1]    0.0094 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001886 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019878 
_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]    0.009157 
_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
E 2 DUD B 1 1280 1280 DUD DUD . 
F 2 DUD D 1 1280 1280 DUD DUD . 
G 2 DUD E 1 1281 1281 DUD DUD . 
#
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 DUD . . . G 2 19.317 15.187 85.422 1 62.38 ? N1 DUD 1281 E 1 
HETATM 2 C C2 DUD . . . G 2 20.493 15.819 85.58 1 63.27 ? C2 DUD 1281 E 1 
HETATM 3 N N3 DUD . . . G 2 20.62 17.14 85.505 1 63.82 ? N3 DUD 1281 E 1 
HETATM 4 C C4 DUD . . . G 2 19.561 17.885 85.24 1 63.42 ? C4 DUD 1281 E 1 
HETATM 5 C C5 DUD . . . G 2 18.331 17.285 85.049 1 63.47 ? C5 DUD 1281 E 1 
HETATM 6 C C6 DUD . . . G 2 18.222 15.896 85.145 1 62.86 ? C6 DUD 1281 E 1 
HETATM 7 O O2 DUD . . . G 2 21.511 15.174 85.828 1 63.61 ? O2 DUD 1281 E 1 
HETATM 8 O O4 DUD . . . G 2 19.686 19.101 85.163 1 60.71 ? O4 DUD 1281 E 1 
HETATM 9 C C1' DUD . . . G 2 19.306 13.741 85.534 1 62.16 ? C1' DUD 1281 E 1 
HETATM 10 C C2' DUD . . . G 2 19.424 13.213 86.933 1 61.88 ? C2' DUD 1281 E 1 
HETATM 11 C C3' DUD . . . G 2 18.758 11.848 86.871 1 61.37 ? C3' DUD 1281 E 1 
HETATM 12 C C4' DUD . . . G 2 17.755 11.954 85.769 1 61.75 ? C4' DUD 1281 E 1 
HETATM 13 O O4' DUD . . . G 2 18.078 13.186 85.164 1 63.03 ? O4' DUD 1281 E 1 
HETATM 14 O O3' DUD . . . G 2 19.674 10.849 86.494 1 60.67 ? O3' DUD 1281 E 1 
HETATM 15 C C5' DUD . . . G 2 16.307 12.05 86.212 1 61.85 ? C5' DUD 1281 E 1 
HETATM 16 O O5' DUD . . . G 2 15.502 12.152 85.044 1 60.51 ? O5' DUD 1281 E 1 
HETATM 17 P PA DUD . . . G 2 14.191 11.492 84.898 1 56.78 ? PA DUD 1281 E 1 
HETATM 18 O O1A DUD . . . G 2 13.427 11.754 86.164 1 57.34 ? O1A DUD 1281 E 1 
HETATM 19 O O2A DUD . . . G 2 13.602 12.12 83.695 1 55.48 ? O2A DUD 1281 E 1 
HETATM 20 O O3A DUD . . . G 2 14.345 10.019 84.528 1 60.3 ? O3A DUD 1281 E 1 
HETATM 21 P PB DUD . . . G 2 13.903 8.745 85.27 1 61.57 ? PB DUD 1281 E 1 
HETATM 22 O O1B DUD . . . G 2 12.519 8.402 84.832 1 60.01 ? O1B DUD 1281 E 1 
HETATM 23 O O2B DUD . . . G 2 14.043 8.787 86.816 1 59.38 ? O2B DUD 1281 E 1 
HETATM 24 O O3B DUD . . . G 2 14.73 7.623 84.697 1 60.31 ? O3B DUD 1281 E 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           241 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           24 
#