data_4C0S # _model_server_result.job_id '_mMQuePmec6Lmnr1ocXpAg' _model_server_result.datetime_utc '2024-11-16 09:37:07' _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 4c0s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 4C0S # _exptl.entry_id 4C0S _exptl.method 'X-RAY DIFFRACTION' # _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 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 4C0S _cell.length_a 135.37 _cell.length_b 135.37 _cell.length_c 304.62 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4C0S _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 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 _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 ? 2 C N N ? 2 E 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 covale ? covale1 A C TYR 162 A TYR 162 1_555 A N SEP 163 A SEP 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale2 A C SEP 163 A SEP 163 1_555 A N GLU 164 A GLU 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale3 A C PRO 238 A PRO 238 1_555 A N TPO 239 A TPO 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale4 A C TPO 239 A TPO 239 1_555 A N ARG 240 A ARG 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? metalc ? metalc1 C O1A GDP . A GDP 500 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc2 C O1B GDP . A GDP 500 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc3 D MG MG . A MG 501 1_555 A OD1 ASP 17 A ASP 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? covale ? covale5 B C TYR 162 B TYR 162 1_555 B N SEP 163 B SEP 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale6 B C SEP 163 B SEP 163 1_555 B N GLU 164 B GLU 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 B C PRO 238 B PRO 238 1_555 B N TPO 239 B TPO 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale8 B C TPO 239 B TPO 239 1_555 B N ARG 240 B ARG 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? metalc ? metalc4 E O1B GDP . B GDP 500 1_555 F MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc5 E O1A GDP . B GDP 500 1_555 F MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? # _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 ? # _atom_sites.entry_id 4C0S _atom_sites.fract_transf_matrix[1][1] 0.007387 _atom_sites.fract_transf_matrix[1][2] 0.004265 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00853 _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] 0.003283 _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 GDP A 1 500 500 GDP GDP . D 3 MG A 1 501 501 MG MG . E 2 GDP B 1 500 500 GDP GDP . F 3 MG B 1 501 501 MG MG . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 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 . . . C 2 -17.324 62.32 182.915 1 40.7 ? PB GDP 500 A 1 HETATM 2 O O1B GDP . . . C 2 -17.305 63.188 181.635 1 47.42 ? O1B GDP 500 A 1 HETATM 3 O O2B GDP . . . C 2 -16.052 62.361 183.68 1 34.51 ? O2B GDP 500 A 1 HETATM 4 O O3B GDP . . . C 2 -17.809 60.892 182.735 1 42.82 ? O3B GDP 500 A 1 HETATM 5 O O3A GDP . . . C 2 -18.479 63.047 183.825 1 35.84 ? O3A GDP 500 A 1 HETATM 6 P PA GDP . . . C 2 -18.106 64.249 184.851 1 37.69 ? PA GDP 500 A 1 HETATM 7 O O1A GDP . . . C 2 -17.187 65.229 184.182 1 49.05 ? O1A GDP 500 A 1 HETATM 8 O O2A GDP . . . C 2 -17.581 63.626 186.121 1 45.66 ? O2A GDP 500 A 1 HETATM 9 O O5' GDP . . . C 2 -19.461 65.059 185.167 1 31.57 ? O5' GDP 500 A 1 HETATM 10 C C5' GDP . . . C 2 -20.636 64.813 184.445 1 34.78 ? C5' GDP 500 A 1 HETATM 11 C C4' GDP . . . C 2 -21.626 65.882 184.846 1 38.6 ? C4' GDP 500 A 1 HETATM 12 O O4' GDP . . . C 2 -22.571 65.355 185.805 1 45.68 ? O4' GDP 500 A 1 HETATM 13 C C3' GDP . . . C 2 -20.926 66.995 185.562 1 43.18 ? C3' GDP 500 A 1 HETATM 14 O O3' GDP . . . C 2 -21.717 68.144 185.291 1 41.68 ? O3' GDP 500 A 1 HETATM 15 C C2' GDP . . . C 2 -21.03 66.646 187.063 1 48.36 ? C2' GDP 500 A 1 HETATM 16 O O2' GDP . . . C 2 -21.19 67.841 187.833 1 49.5 ? O2' GDP 500 A 1 HETATM 17 C C1' GDP . . . C 2 -22.312 65.833 187.152 1 47.39 ? C1' GDP 500 A 1 HETATM 18 N N9 GDP . . . C 2 -22.266 64.686 188.102 1 45.73 ? N9 GDP 500 A 1 HETATM 19 C C8 GDP . . . C 2 -21.302 63.743 188.207 1 49.91 ? C8 GDP 500 A 1 HETATM 20 N N7 GDP . . . C 2 -21.64 62.798 189.134 1 44.29 ? N7 GDP 500 A 1 HETATM 21 C C5 GDP . . . C 2 -22.849 63.14 189.627 1 43.52 ? C5 GDP 500 A 1 HETATM 22 C C6 GDP . . . C 2 -23.806 62.595 190.645 1 42.99 ? C6 GDP 500 A 1 HETATM 23 O O6 GDP . . . C 2 -23.567 61.539 191.296 1 40.08 ? O6 GDP 500 A 1 HETATM 24 N N1 GDP . . . C 2 -24.966 63.252 190.798 1 37.82 ? N1 GDP 500 A 1 HETATM 25 C C2 GDP . . . C 2 -25.239 64.367 190.103 1 33.74 ? C2 GDP 500 A 1 HETATM 26 N N2 GDP . . . C 2 -26.377 65.014 190.321 1 33.27 ? N2 GDP 500 A 1 HETATM 27 N N3 GDP . . . C 2 -24.421 64.892 189.201 1 33.69 ? N3 GDP 500 A 1 HETATM 28 C C4 GDP . . . C 2 -23.25 64.347 188.918 1 38.65 ? C4 GDP 500 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #