data_3A6U
#
_model_server_result.job_id            FrKZMF-dMniCnB9Fp9DWRg 
_model_server_result.datetime_utc      '2024-10-11 17:32:46' 
_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          3a6u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":5001}' 
#
_entry.id    3A6U 
#
_exptl.entry_id    3A6U 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              363.221 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            3A6U 
_cell.length_a            38.234 
_cell.length_b            56.003 
_cell.length_c            59.339 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3A6U 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C10 H14 N5 O8 P' 
_chem_comp.formula_weight    363.221 
_chem_comp.id                8OG 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" 
_chem_comp.type              'dna linking' 
_chem_comp.pdbx_synonyms     "8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" 
#
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
OP3 P 8OG sing 1 n n 
OP3 HOP3 8OG sing 2 n n 
P OP1 8OG doub 3 n n 
P OP2 8OG sing 4 n n 
P O5' 8OG sing 5 n n 
OP2 HOP2 8OG sing 6 n n 
O5' C5' 8OG sing 7 n n 
C5' C4' 8OG sing 8 n n 
C5' H5' 8OG sing 9 n n 
C5' "H5''" 8OG sing 10 n n 
C4' O4' 8OG sing 11 n n 
C4' C3' 8OG sing 12 n n 
C4' H4' 8OG sing 13 n n 
O4' C1' 8OG sing 14 n n 
C3' O3' 8OG sing 15 n n 
C3' C2' 8OG sing 16 n n 
C3' H3' 8OG sing 17 n n 
O3' HO3' 8OG sing 18 n n 
C2' C1' 8OG sing 19 n n 
C2' H2' 8OG sing 20 n n 
C2' "H2''" 8OG sing 21 n n 
C1' N9 8OG sing 22 n n 
C1' H1' 8OG sing 23 n n 
N9 C8 8OG sing 24 n n 
N9 C4 8OG sing 25 n n 
C8 N7 8OG sing 26 n n 
C8 O8 8OG doub 27 n n 
N7 C5 8OG sing 28 n n 
N7 H7 8OG sing 29 n n 
C5 C6 8OG sing 30 n n 
C5 C4 8OG doub 31 n n 
C6 O6 8OG doub 32 n n 
C6 N1 8OG sing 33 n n 
N1 C2 8OG sing 34 n n 
N1 H1 8OG sing 35 n n 
C2 N2 8OG sing 36 n n 
C2 N3 8OG doub 37 n n 
N2 H21 8OG sing 38 n n 
N2 H22 8OG sing 39 n n 
N3 C4 8OG sing 40 n n 
#
_atom_sites.entry_id                     3A6U 
_atom_sites.fract_transf_matrix[1][1]    0.026155 
_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]    0.017856 
_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]    0.016852 
_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
B 2 MN A 1 1001 1001 MN MN . 
C 3 SO4 A 1 2001 2001 SO4 SO4 . 
D 4 8OG A 1 5001 5001 8OG G42 . 
E 5 HOH A 1 130 130 HOH HOH . 
E 5 HOH A 2 131 131 HOH HOH . 
E 5 HOH A 3 132 132 HOH HOH . 
E 5 HOH A 4 133 133 HOH HOH . 
E 5 HOH A 5 134 134 HOH HOH . 
E 5 HOH A 6 135 135 HOH HOH . 
E 5 HOH A 7 136 136 HOH HOH . 
E 5 HOH A 8 137 137 HOH HOH . 
E 5 HOH A 9 138 138 HOH HOH . 
E 5 HOH A 10 139 139 HOH HOH . 
E 5 HOH A 11 140 140 HOH HOH . 
E 5 HOH A 12 141 141 HOH HOH . 
E 5 HOH A 13 142 142 HOH HOH . 
E 5 HOH A 14 143 143 HOH HOH . 
E 5 HOH A 15 144 144 HOH HOH . 
E 5 HOH A 16 145 145 HOH HOH . 
E 5 HOH A 17 146 146 HOH HOH . 
E 5 HOH A 18 147 147 HOH HOH . 
E 5 HOH A 19 148 148 HOH HOH . 
E 5 HOH A 20 149 149 HOH HOH . 
E 5 HOH A 21 150 150 HOH HOH . 
E 5 HOH A 22 151 151 HOH HOH . 
E 5 HOH A 23 152 152 HOH HOH . 
E 5 HOH A 24 153 153 HOH HOH . 
E 5 HOH A 25 154 154 HOH HOH . 
E 5 HOH A 26 155 155 HOH HOH . 
E 5 HOH A 27 156 156 HOH HOH . 
E 5 HOH A 28 157 157 HOH HOH . 
E 5 HOH A 29 158 158 HOH HOH . 
E 5 HOH A 30 159 159 HOH HOH . 
E 5 HOH A 31 160 160 HOH HOH . 
E 5 HOH A 32 161 161 HOH HOH . 
E 5 HOH A 33 162 162 HOH HOH . 
E 5 HOH A 34 163 163 HOH HOH . 
E 5 HOH A 35 164 164 HOH HOH . 
E 5 HOH A 36 165 165 HOH HOH . 
E 5 HOH A 37 166 166 HOH HOH . 
E 5 HOH A 38 167 167 HOH HOH . 
E 5 HOH A 39 168 168 HOH HOH . 
E 5 HOH A 40 169 169 HOH HOH . 
E 5 HOH A 41 170 170 HOH HOH . 
E 5 HOH A 42 171 171 HOH HOH . 
E 5 HOH A 43 172 172 HOH HOH . 
E 5 HOH A 44 173 173 HOH HOH . 
E 5 HOH A 45 174 174 HOH HOH . 
E 5 HOH A 46 175 175 HOH HOH . 
E 5 HOH A 47 176 176 HOH HOH . 
E 5 HOH A 48 177 177 HOH HOH . 
E 5 HOH A 49 178 178 HOH HOH . 
E 5 HOH A 50 179 179 HOH HOH . 
E 5 HOH A 51 180 180 HOH HOH . 
E 5 HOH A 52 181 181 HOH HOH . 
E 5 HOH A 53 182 182 HOH HOH . 
E 5 HOH A 54 183 183 HOH HOH . 
E 5 HOH A 55 184 184 HOH HOH . 
E 5 HOH A 56 185 185 HOH HOH . 
E 5 HOH A 57 186 186 HOH HOH . 
E 5 HOH A 58 187 187 HOH HOH . 
E 5 HOH A 59 188 188 HOH HOH . 
E 5 HOH A 60 189 189 HOH HOH . 
E 5 HOH A 61 190 190 HOH HOH . 
E 5 HOH A 62 191 191 HOH HOH . 
E 5 HOH A 63 192 192 HOH HOH . 
E 5 HOH A 64 193 193 HOH HOH . 
E 5 HOH A 65 194 194 HOH HOH . 
E 5 HOH A 66 195 195 HOH HOH . 
E 5 HOH A 67 196 196 HOH HOH . 
E 5 HOH A 68 197 197 HOH HOH . 
E 5 HOH A 69 198 198 HOH HOH . 
E 5 HOH A 70 199 199 HOH HOH . 
E 5 HOH A 71 200 200 HOH HOH . 
E 5 HOH A 72 201 201 HOH HOH . 
E 5 HOH A 73 202 202 HOH HOH . 
E 5 HOH A 74 203 203 HOH HOH . 
E 5 HOH A 75 204 204 HOH HOH . 
E 5 HOH A 76 205 1 HOH HOH . 
E 5 HOH A 77 206 206 HOH HOH . 
E 5 HOH A 78 207 207 HOH HOH . 
E 5 HOH A 79 208 208 HOH HOH . 
E 5 HOH A 80 209 209 HOH HOH . 
E 5 HOH A 81 210 210 HOH HOH . 
E 5 HOH A 82 211 211 HOH HOH . 
E 5 HOH A 83 212 212 HOH HOH . 
E 5 HOH A 84 213 213 HOH HOH . 
E 5 HOH A 85 214 214 HOH HOH . 
E 5 HOH A 86 215 215 HOH HOH . 
E 5 HOH A 87 216 216 HOH HOH . 
E 5 HOH A 88 217 2 HOH HOH . 
E 5 HOH A 89 218 3 HOH HOH . 
E 5 HOH A 90 221 221 HOH HOH . 
E 5 HOH A 91 222 222 HOH HOH . 
E 5 HOH A 92 223 223 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 O OP3 8OG . . . D 4 -9.769 2.267 24.489 1 23.44 ? OP3 8OG 5001 A 1 
HETATM 2 P P 8OG . . . D 4 -9.544 1.32 23.374 1 21.6 ? P 8OG 5001 A 1 
HETATM 3 O OP1 8OG . . . D 4 -8.459 1.904 22.546 1 23.19 ? OP1 8OG 5001 A 1 
HETATM 4 O OP2 8OG . . . D 4 -10.863 1.058 22.748 1 22.78 ? OP2 8OG 5001 A 1 
HETATM 5 O O5' 8OG . . . D 4 -9.028 -0.078 24.016 1 23.35 ? O5' 8OG 5001 A 1 
HETATM 6 C C5' 8OG . . . D 4 -7.731 -0.185 24.632 1 17.87 ? C5' 8OG 5001 A 1 
HETATM 7 C C4' 8OG . . . D 4 -7.775 -1.006 25.928 1 15.05 ? C4' 8OG 5001 A 1 
HETATM 8 O O4' 8OG . . . D 4 -6.45 -1.443 26.304 1 13.92 ? O4' 8OG 5001 A 1 
HETATM 9 C C3' 8OG . . . D 4 -8.317 -0.199 27.106 1 15.37 ? C3' 8OG 5001 A 1 
HETATM 10 O O3' 8OG . . . D 4 -9.15 -1.029 27.938 1 14.96 ? O3' 8OG 5001 A 1 
HETATM 11 C C2' 8OG . . . D 4 -7.097 0.289 27.828 1 13.95 ? C2' 8OG 5001 A 1 
HETATM 12 C C1' 8OG . . . D 4 -6.063 -0.795 27.55 1 15.12 ? C1' 8OG 5001 A 1 
HETATM 13 N N9 8OG . . . D 4 -4.689 -0.225 27.426 1 12.69 ? N9 8OG 5001 A 1 
HETATM 14 C C8 8OG . . . D 4 -3.693 -0.425 28.345 1 10.57 ? C8 8OG 5001 A 1 
HETATM 15 N N7 8OG . . . D 4 -2.581 0.133 28.077 1 9.16 ? N7 8OG 5001 A 1 
HETATM 16 C C5 8OG . . . D 4 -2.783 0.795 26.864 1 9.1 ? C5 8OG 5001 A 1 
HETATM 17 C C6 8OG . . . D 4 -1.925 1.598 26.039 1 8.03 ? C6 8OG 5001 A 1 
HETATM 18 O O6 8OG . . . D 4 -0.75 1.9 26.224 1 9.14 ? O6 8OG 5001 A 1 
HETATM 19 N N1 8OG . . . D 4 -2.588 2.061 24.886 1 5.47 ? N1 8OG 5001 A 1 
HETATM 20 C C2 8OG . . . D 4 -3.911 1.795 24.552 1 4.4 ? C2 8OG 5001 A 1 
HETATM 21 N N2 8OG . . . D 4 -4.364 2.318 23.413 1 5.97 ? N2 8OG 5001 A 1 
HETATM 22 N N3 8OG . . . D 4 -4.722 1.043 25.319 1 7.74 ? N3 8OG 5001 A 1 
HETATM 23 C C4 8OG . . . D 4 -4.112 0.575 26.447 1 9.13 ? C4 8OG 5001 A 1 
HETATM 24 O O8 8OG . . . D 4 -3.93 -1.108 29.339 1 7.94 ? O8 8OG 5001 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           24 
#