data_4XC8 # _model_server_result.job_id Ni3S32kMe7wKbX2XBoOgvg _model_server_result.datetime_utc '2024-11-24 14:04:48' _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 4xc8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1102}' # _entry.id 4XC8 # _exptl.entry_id 4XC8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 4XC8 _cell.length_a 316.51 _cell.length_b 316.51 _cell.length_c 342.27 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XC8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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 _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 H N 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 metalc ? metalc1 A OG SER 243 A SER 223 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? metalc ? metalc2 A O ILE 268 A ILE 248 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc3 A OD1 ASP 269 A ASP 249 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc4 A OD1 ASP 282 A ASP 262 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc5 A OD1 ASP 282 A ASP 262 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? metalc ? metalc6 A OD2 ASP 282 A ASP 262 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc7 A OE1 GLU 330 A GLU 310 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc8 D O2B GDP . A GDP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc9 B OG SER 243 B SER 223 1_555 I MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc10 B O ILE 268 B ILE 248 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc11 B OD1 ASP 269 B ASP 249 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc12 B OD1 ASP 282 B ASP 262 1_555 I MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc13 B OD1 ASP 282 B ASP 262 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? metalc ? metalc14 B OD2 ASP 282 B ASP 262 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? metalc ? metalc15 B OE1 GLU 330 B GLU 310 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? # _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 180 n n PB O2B GDP sing 181 n n PB O3B GDP sing 182 n n PB O3A GDP sing 183 n n O2B HOB2 GDP sing 184 n n O3B HOB3 GDP sing 185 n n O3A PA GDP sing 186 n n PA O1A GDP doub 187 n n PA O2A GDP sing 188 n n PA O5' GDP sing 189 n n O2A HOA2 GDP sing 190 n n O5' C5' GDP sing 191 n n C5' C4' GDP sing 192 n n C5' H5' GDP sing 193 n n C5' "H5''" GDP sing 194 n n C4' O4' GDP sing 195 n n C4' C3' GDP sing 196 n n C4' H4' GDP sing 197 n n O4' C1' GDP sing 198 n n C3' O3' GDP sing 199 n n C3' C2' GDP sing 200 n n C3' H3' GDP sing 201 n n O3' HO3' GDP sing 202 n n C2' O2' GDP sing 203 n n C2' C1' GDP sing 204 n n C2' H2' GDP sing 205 n n O2' HO2' GDP sing 206 n n C1' N9 GDP sing 207 n n C1' H1' GDP sing 208 n n N9 C8 GDP sing 209 n y N9 C4 GDP sing 210 n y C8 N7 GDP doub 211 n y C8 H8 GDP sing 212 n n N7 C5 GDP sing 213 n y C5 C6 GDP sing 214 n n C5 C4 GDP doub 215 n y C6 O6 GDP doub 216 n n C6 N1 GDP sing 217 n n N1 C2 GDP sing 218 n n N1 HN1 GDP sing 219 n n C2 N2 GDP sing 220 n n C2 N3 GDP doub 221 n n N2 HN21 GDP sing 222 n n N2 HN22 GDP sing 223 n n N3 C4 GDP sing 224 n n # _atom_sites.entry_id 4XC8 _atom_sites.fract_transf_matrix[1][1] 0.003159 _atom_sites.fract_transf_matrix[1][2] 0.001824 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003648 _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] 0.002922 _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 BCO A 1 1101 1211 BCO BCO . D 3 GDP A 1 1102 1200 GDP GDP . E 4 MG A 1 1103 1 MG MG . F 4 MG A 1 1104 3 MG MG . G 2 BCO B 1 1101 1212 BCO BCO . H 3 GDP B 1 1102 1201 GDP GDP . I 4 MG B 1 1103 2 MG MG . J 4 MG B 1 1104 4 MG MG . # 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 . . . D 3 -188.712 -77.488 5.851 1 94.42 ? PB GDP 1102 A 1 HETATM 2 O O1B GDP . . . D 3 -189.939 -76.752 5.55 1 93.72 ? O1B GDP 1102 A 1 HETATM 3 O O2B GDP . . . D 3 -188.903 -78.32 7.122 1 96.55 ? O2B GDP 1102 A 1 HETATM 4 O O3B GDP . . . D 3 -187.553 -76.487 6.064 1 93.95 ? O3B GDP 1102 A 1 HETATM 5 O O3A GDP . . . D 3 -188.336 -78.414 4.656 1 73.81 ? O3A GDP 1102 A 1 HETATM 6 P PA GDP . . . D 3 -189.32 -79.53 4.099 1 79.21 ? PA GDP 1102 A 1 HETATM 7 O O1A GDP . . . D 3 -188.836 -80.896 4.514 1 73.25 ? O1A GDP 1102 A 1 HETATM 8 O O2A GDP . . . D 3 -190.642 -79.343 4.596 1 80.63 ? O2A GDP 1102 A 1 HETATM 9 O O5' GDP . . . D 3 -189.304 -79.471 2.534 1 85.22 ? O5' GDP 1102 A 1 HETATM 10 C C5' GDP . . . D 3 -190.094 -78.694 1.869 1 79.98 ? C5' GDP 1102 A 1 HETATM 11 C C4' GDP . . . D 3 -190.548 -79.438 0.594 1 76.32 ? C4' GDP 1102 A 1 HETATM 12 O O4' GDP . . . D 3 -189.445 -79.595 -0.387 1 75.05 ? O4' GDP 1102 A 1 HETATM 13 C C3' GDP . . . D 3 -191.104 -80.79 0.792 1 76.99 ? C3' GDP 1102 A 1 HETATM 14 O O3' GDP . . . D 3 -192.263 -81.009 0.024 1 77.78 ? O3' GDP 1102 A 1 HETATM 15 C C2' GDP . . . D 3 -190.058 -81.689 0.322 1 77.91 ? C2' GDP 1102 A 1 HETATM 16 O O2' GDP . . . D 3 -190.545 -82.959 -0.159 1 81.25 ? O2' GDP 1102 A 1 HETATM 17 C C1' GDP . . . D 3 -189.421 -80.932 -0.781 1 78.27 ? C1' GDP 1102 A 1 HETATM 18 N N9 GDP . . . D 3 -188.028 -81.36 -1.098 1 86.3 ? N9 GDP 1102 A 1 HETATM 19 C C8 GDP . . . D 3 -187.15 -81.733 -0.24 1 89.16 ? C8 GDP 1102 A 1 HETATM 20 N N7 GDP . . . D 3 -186.026 -82.038 -0.87 1 92.73 ? N7 GDP 1102 A 1 HETATM 21 C C5 GDP . . . D 3 -186.219 -81.847 -2.182 1 92.07 ? C5 GDP 1102 A 1 HETATM 22 C C6 GDP . . . D 3 -185.381 -82.008 -3.346 1 90.98 ? C6 GDP 1102 A 1 HETATM 23 O O6 GDP . . . D 3 -184.095 -82.441 -3.195 1 88.75 ? O6 GDP 1102 A 1 HETATM 24 N N1 GDP . . . D 3 -185.871 -81.73 -4.564 1 94.11 ? N1 GDP 1102 A 1 HETATM 25 C C2 GDP . . . D 3 -187.076 -81.323 -4.689 1 96.67 ? C2 GDP 1102 A 1 HETATM 26 N N2 GDP . . . D 3 -187.585 -81.024 -6.045 1 99.27 ? N2 GDP 1102 A 1 HETATM 27 N N3 GDP . . . D 3 -187.914 -81.156 -3.591 1 96.42 ? N3 GDP 1102 A 1 HETATM 28 C C4 GDP . . . D 3 -187.467 -81.423 -2.347 1 92.37 ? C4 GDP 1102 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #