data_7XKJ # _model_server_result.job_id Z7nsKVx7Kzb78Scn9-zrXw _model_server_result.datetime_utc '2025-07-05 09:48:51' _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 7xkj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 7XKJ # _exptl.entry_id 7XKJ _exptl.method 'ELECTRON CRYSTALLOGRAPHY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 7XKJ _cell.length_a 38.88 _cell.length_b 49.28 _cell.length_c 87.2 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7XKJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 2 _struct_asym.id B _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 covale ? covale1 A OE1 GLU 168 A GLU 168 1_555 B N3 GDP . A GDP 201 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 1.182 ? metalc ? metalc1 A OG SER 17 A SER 17 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc2 B O3B GDP . A GDP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 165 n n PB O2B GDP sing 166 n n PB O3B GDP sing 167 n n PB O3A GDP sing 168 n n O2B HOB2 GDP sing 169 n n O3B HOB3 GDP sing 170 n n O3A PA GDP sing 171 n n PA O1A GDP doub 172 n n PA O2A GDP sing 173 n n PA O5' GDP sing 174 n n O2A HOA2 GDP sing 175 n n O5' C5' GDP sing 176 n n C5' C4' GDP sing 177 n n C5' H5' GDP sing 178 n n C5' "H5''" GDP sing 179 n n C4' O4' GDP sing 180 n n C4' C3' GDP sing 181 n n C4' H4' GDP sing 182 n n O4' C1' GDP sing 183 n n C3' O3' GDP sing 184 n n C3' C2' GDP sing 185 n n C3' H3' GDP sing 186 n n O3' HO3' GDP sing 187 n n C2' O2' GDP sing 188 n n C2' C1' GDP sing 189 n n C2' H2' GDP sing 190 n n O2' HO2' GDP sing 191 n n C1' N9 GDP sing 192 n n C1' H1' GDP sing 193 n n N9 C8 GDP sing 194 n y N9 C4 GDP sing 195 n y C8 N7 GDP doub 196 n y C8 H8 GDP sing 197 n n N7 C5 GDP sing 198 n y C5 C6 GDP sing 199 n n C5 C4 GDP doub 200 n y C6 O6 GDP doub 201 n n C6 N1 GDP sing 202 n n N1 C2 GDP sing 203 n n N1 HN1 GDP sing 204 n n C2 N2 GDP sing 205 n n C2 N3 GDP doub 206 n n N2 HN21 GDP sing 207 n n N2 HN22 GDP sing 208 n n N3 C4 GDP sing 209 n n # _atom_sites.entry_id 7XKJ _atom_sites.fract_transf_matrix[1][1] 0.02572 _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] 0.020292 _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] 0.011468 _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 GDP A 1 201 201 GDP GDP . C 3 6IC A 1 202 202 6IC 6IC . D 4 MG A 1 203 203 MG MG . E 5 HOH A 1 301 15 HOH HOH . E 5 HOH A 2 302 13 HOH HOH . E 5 HOH A 3 303 10 HOH HOH . E 5 HOH A 4 304 11 HOH HOH . E 5 HOH A 5 305 16 HOH HOH . E 5 HOH A 6 306 12 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 P PB GDP . . . B 2 8.288 -3.101 -15.749 1 17.93 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 9.426 -2.851 -16.7 1 15.35 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 7.52 -1.872 -15.353 1 24.22 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 7.417 -4.256 -16.129 1 18.21 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 8.976 -3.486 -14.353 1 20.16 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 9.774 -4.837 -14.011 1 26.11 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 10.593 -5.29 -15.191 1 23.57 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 8.849 -5.796 -13.327 1 22.37 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 10.767 -4.287 -12.89 1 19.06 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 12.082 -3.909 -13.262 1 25.56 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 13.011 -4.272 -12.122 1 31.95 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 12.461 -3.764 -10.914 1 31.56 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 13.137 -5.778 -11.959 1 38.6 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 14.495 -6.175 -12.161 1 37.08 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 12.741 -6.082 -10.536 1 26.97 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 13.795 -6.808 -9.907 1 26.59 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 12.591 -4.728 -9.876 1 26.67 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 11.392 -4.683 -9.021 1 23.35 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 10.111 -4.701 -9.405 1 27.12 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 9.283 -4.639 -8.334 1 22.38 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 10.055 -4.579 -7.242 1 21.77 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 9.852 -4.492 -5.787 1 26.35 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 8.708 -4.461 -5.308 1 27.87 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 10.929 -4.437 -5.004 1 18.21 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 12.174 -4.468 -5.497 1 27.68 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 13.221 -4.419 -4.651 1 35.6 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 12.44 -4.547 -6.814 1 28.99 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 11.438 -4.601 -7.707 1 22.31 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #