data_2A5B # _model_server_result.job_id 4xmPua2FSbX2ujN2Zh6WRA _model_server_result.datetime_utc '2024-11-05 01:14:09' _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 2a5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":255}' # _entry.id 2A5B # _exptl.entry_id 2A5B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 283.241 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXY-8-OXOGUANOSINE" _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 2A5B _cell.length_a 70.019 _cell.length_b 79.487 _cell.length_c 42.909 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2A5B _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 79.487 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 A SG CYS 4 A CYS 4 1_555 A SG CYS 83 A CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 B SG CYS 4 B CYS 4 1_555 B SG CYS 83 B CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? covale ? covale1 A ND2 ASN 17 A ASN 17 1_555 C C1 NAG . A NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 B ND2 ASN 17 B ASN 17 1_555 E C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _chem_comp.formula 'C10 H13 N5 O5' _chem_comp.formula_weight 283.241 _chem_comp.id 8HG _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXY-8-OXOGUANOSINE" _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 O6 C6 8HG doub 1 n n C6 N1 8HG sing 2 n n C6 C5 8HG sing 3 n n N1 C2 8HG sing 4 n n N1 HN1 8HG sing 5 n n C2 N2 8HG sing 6 n n C2 N3 8HG doub 7 n n N2 HN21 8HG sing 8 n n N2 HN22 8HG sing 9 n n N3 C4 8HG sing 10 n n C4 C5 8HG doub 11 n n C4 N9 8HG sing 12 n n C5 N7 8HG sing 13 n n N7 C8 8HG sing 14 n n C8 O20 8HG doub 15 n n C8 N9 8HG sing 16 n n N9 C1' 8HG sing 17 n n C1' O4' 8HG sing 18 n n C1' C2' 8HG sing 19 n n C1' H1' 8HG sing 20 n n O4' C4' 8HG sing 21 n n C2' C3' 8HG sing 22 n n C2' "H2'1" 8HG sing 23 n n C2' "H2'2" 8HG sing 24 n n C3' O3' 8HG sing 25 n n C3' C4' 8HG sing 26 n n C3' H3' 8HG sing 27 n n O3' H1 8HG sing 28 n n C4' C5' 8HG sing 29 n n C4' H4' 8HG sing 30 n n C5' O5' 8HG sing 31 n n C5' "H5'1" 8HG sing 32 n n C5' "H5'2" 8HG sing 33 n n O5' H5' 8HG sing 34 n n N7 H13 8HG sing 35 n n # _atom_sites.entry_id 2A5B _atom_sites.fract_transf_matrix[1][1] 0.014282 _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] 0.012581 _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] 0.023305 _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 NAG A 1 201 201 NAG NAG . D 3 8HG A 1 255 255 8HG 8HG . E 2 NAG B 1 201 201 NAG NAG . F 4 HOH A 1 256 2 HOH HOH . F 4 HOH A 2 257 5 HOH HOH . F 4 HOH A 3 258 7 HOH HOH . F 4 HOH A 4 259 8 HOH HOH . F 4 HOH A 5 260 10 HOH HOH . F 4 HOH A 6 261 11 HOH HOH . F 4 HOH A 7 262 16 HOH HOH . F 4 HOH A 8 263 21 HOH HOH . F 4 HOH A 9 264 22 HOH HOH . F 4 HOH A 10 265 24 HOH HOH . F 4 HOH A 11 266 25 HOH HOH . F 4 HOH A 12 267 26 HOH HOH . F 4 HOH A 13 268 28 HOH HOH . F 4 HOH A 14 269 46 HOH HOH . F 4 HOH A 15 270 50 HOH HOH . F 4 HOH A 16 271 51 HOH HOH . F 4 HOH A 17 272 53 HOH HOH . F 4 HOH A 18 273 54 HOH HOH . F 4 HOH A 19 274 65 HOH HOH . G 4 HOH B 1 202 1 HOH HOH . G 4 HOH B 2 203 4 HOH HOH . G 4 HOH B 3 204 6 HOH HOH . G 4 HOH B 4 205 12 HOH HOH . G 4 HOH B 5 206 13 HOH HOH . G 4 HOH B 6 207 14 HOH HOH . G 4 HOH B 7 208 15 HOH HOH . G 4 HOH B 8 209 19 HOH HOH . G 4 HOH B 9 210 20 HOH HOH . G 4 HOH B 10 211 27 HOH HOH . G 4 HOH B 11 212 31 HOH HOH . G 4 HOH B 12 213 34 HOH HOH . G 4 HOH B 13 214 35 HOH HOH . G 4 HOH B 14 215 38 HOH HOH . G 4 HOH B 15 216 40 HOH HOH . G 4 HOH B 16 217 41 HOH HOH . G 4 HOH B 17 218 52 HOH HOH . G 4 HOH B 18 219 56 HOH HOH . G 4 HOH B 19 220 57 HOH HOH . G 4 HOH B 20 221 60 HOH HOH . G 4 HOH B 21 222 61 HOH HOH . G 4 HOH B 22 223 62 HOH HOH . G 4 HOH B 23 224 63 HOH HOH . G 4 HOH B 24 225 64 HOH HOH . G 4 HOH B 25 226 66 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 O6 8HG . . . D 3 -0.345 27.796 0.004 1 72.97 ? O6 8HG 255 A 1 HETATM 2 C C6 8HG . . . D 3 0.521 28.301 -0.75 1 72.28 ? C6 8HG 255 A 1 HETATM 3 N N1 8HG . . . D 3 1.344 29.215 -0.23 1 71.79 ? N1 8HG 255 A 1 HETATM 4 C C2 8HG . . . D 3 2.287 29.772 -0.991 1 71.72 ? C2 8HG 255 A 1 HETATM 5 N N2 8HG . . . D 3 3.117 30.671 -0.513 1 72.41 ? N2 8HG 255 A 1 HETATM 6 N N3 8HG . . . D 3 2.471 29.477 -2.276 1 73.04 ? N3 8HG 255 A 1 HETATM 7 C C4 8HG . . . D 3 1.667 28.563 -2.859 1 73.34 ? C4 8HG 255 A 1 HETATM 8 C C5 8HG . . . D 3 0.654 27.937 -2.104 1 72.82 ? C5 8HG 255 A 1 HETATM 9 N N7 8HG . . . D 3 0.008 27.075 -2.935 1 72.88 ? N7 8HG 255 A 1 HETATM 10 C C8 8HG . . . D 3 0.635 27.219 -4.113 1 72.54 ? C8 8HG 255 A 1 HETATM 11 O O20 8HG . . . D 3 0.288 26.566 -5.164 1 71.7 ? O20 8HG 255 A 1 HETATM 12 N N9 8HG . . . D 3 1.647 28.105 -4.11 1 72.99 ? N9 8HG 255 A 1 HETATM 13 C C1' 8HG . . . D 3 2.544 28.502 -5.243 1 73.56 ? C1' 8HG 255 A 1 HETATM 14 O O4' 8HG . . . D 3 3.733 29.284 -4.976 1 73.04 ? O4' 8HG 255 A 1 HETATM 15 C C2' 8HG . . . D 3 1.744 29.349 -6.227 1 75.99 ? C2' 8HG 255 A 1 HETATM 16 C C3' 8HG . . . D 3 2.782 30.211 -6.916 1 74.99 ? C3' 8HG 255 A 1 HETATM 17 O O3' 8HG . . . D 3 2.675 29.882 -8.303 1 75.84 ? O3' 8HG 255 A 1 HETATM 18 C C4' 8HG . . . D 3 4.1 29.761 -6.281 1 73.44 ? C4' 8HG 255 A 1 HETATM 19 C C5' 8HG . . . D 3 5.185 30.818 -6.307 1 72.23 ? C5' 8HG 255 A 1 HETATM 20 O O5' 8HG . . . D 3 4.756 31.9 -7.152 1 74.75 ? O5' 8HG 255 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #