data_4C0S # _model_server_result.job_id QpuIsFMlBt9g4gVyIRbF6A _model_server_result.datetime_utc '2024-11-16 09:37:26' _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":"E","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 . . . E 2 26.682 52.402 161.534 1 38.38 ? PB GDP 500 B 1 HETATM 2 O O1B GDP . . . E 2 25.788 53.384 160.745 1 43.99 ? O1B GDP 500 B 1 HETATM 3 O O2B GDP . . . E 2 25.85 51.241 162.004 1 32.18 ? O2B GDP 500 B 1 HETATM 4 O O3B GDP . . . E 2 27.692 53.092 162.444 1 30.49 ? O3B GDP 500 B 1 HETATM 5 O O3A GDP . . . E 2 27.728 51.721 160.472 1 38.95 ? O3A GDP 500 B 1 HETATM 6 P PA GDP . . . E 2 27.531 50.27 159.771 1 38.4 ? PA GDP 500 B 1 HETATM 7 O O1A GDP . . . E 2 26.379 50.13 158.807 1 35.14 ? O1A GDP 500 B 1 HETATM 8 O O2A GDP . . . E 2 27.674 49.188 160.802 1 44.06 ? O2A GDP 500 B 1 HETATM 9 O O5' GDP . . . E 2 28.865 50.366 158.921 1 49.24 ? O5' GDP 500 B 1 HETATM 10 C C5' GDP . . . E 2 29.196 51.499 158.068 1 49.54 ? C5' GDP 500 B 1 HETATM 11 C C4' GDP . . . E 2 29.966 50.95 156.837 1 45.83 ? C4' GDP 500 B 1 HETATM 12 O O4' GDP . . . E 2 31.302 50.576 157.214 1 39.08 ? O4' GDP 500 B 1 HETATM 13 C C3' GDP . . . E 2 29.335 49.657 156.303 1 40.19 ? C3' GDP 500 B 1 HETATM 14 O O3' GDP . . . E 2 29.606 49.545 154.913 1 43.65 ? O3' GDP 500 B 1 HETATM 15 C C2' GDP . . . E 2 30.133 48.586 156.942 1 37.07 ? C2' GDP 500 B 1 HETATM 16 O O2' GDP . . . E 2 30.151 47.438 156.143 1 36.87 ? O2' GDP 500 B 1 HETATM 17 C C1' GDP . . . E 2 31.492 49.181 156.965 1 40.75 ? C1' GDP 500 B 1 HETATM 18 N N9 GDP . . . E 2 32.257 48.635 158.068 1 48.94 ? N9 GDP 500 B 1 HETATM 19 C C8 GDP . . . E 2 31.824 48.431 159.334 1 56.26 ? C8 GDP 500 B 1 HETATM 20 N N7 GDP . . . E 2 32.82 47.953 160.123 1 56.37 ? N7 GDP 500 B 1 HETATM 21 C C5 GDP . . . E 2 33.904 47.875 159.343 1 55.72 ? C5 GDP 500 B 1 HETATM 22 C C6 GDP . . . E 2 35.273 47.447 159.53 1 52.81 ? C6 GDP 500 B 1 HETATM 23 O O6 GDP . . . E 2 35.658 47.074 160.631 1 52.3 ? O6 GDP 500 B 1 HETATM 24 N N1 GDP . . . E 2 36.104 47.514 158.489 1 64.62 ? N1 GDP 500 B 1 HETATM 25 C C2 GDP . . . E 2 35.727 47.957 157.271 1 58.64 ? C2 GDP 500 B 1 HETATM 26 N N2 GDP . . . E 2 36.64 47.962 156.292 1 66.98 ? N2 GDP 500 B 1 HETATM 27 N N3 GDP . . . E 2 34.464 48.366 156.999 1 59.87 ? N3 GDP 500 B 1 HETATM 28 C C4 GDP . . . E 2 33.533 48.336 157.998 1 58.42 ? C4 GDP 500 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #