data_5FR2 # _model_server_result.job_id '_VnnZ5Hp_U04stjoV7lpbg' _model_server_result.datetime_utc '2024-10-11 06:16:53' _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 5fr2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1192}' # _entry.id 5FR2 # _exptl.entry_id 5FR2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 120 _cell.entry_id 5FR2 _cell.length_a 176.979 _cell.length_b 176.979 _cell.length_c 63.896 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5FR2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 62' # _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 # _struct_asym.details ? _struct_asym.entity_id 4 _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 covale ? covale1 A SG CYS 192 A CYS 190 1_555 C C1 FAR . A FAR 1190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? covale ? covale2 B C ILE 186 B ILE 177 1_555 B N ALY 187 B ALY 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 B C ALY 187 B ALY 178 1_555 B N SER 188 B SER 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OG1 THR 21 A THR 19 1_555 E MG MG . A MG 1193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc2 A O THR 39 A THR 37 1_555 E MG MG . A MG 1193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc3 D O3B GDP . A GDP 1192 1_555 E MG MG . A MG 1193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc4 E MG MG . A MG 1193 1_555 G O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? # _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 175 n n PB O2B GDP sing 176 n n PB O3B GDP sing 177 n n PB O3A GDP sing 178 n n O2B HOB2 GDP sing 179 n n O3B HOB3 GDP sing 180 n n O3A PA GDP sing 181 n n PA O1A GDP doub 182 n n PA O2A GDP sing 183 n n PA O5' GDP sing 184 n n O2A HOA2 GDP sing 185 n n O5' C5' GDP sing 186 n n C5' C4' GDP sing 187 n n C5' H5' GDP sing 188 n n C5' "H5''" GDP sing 189 n n C4' O4' GDP sing 190 n n C4' C3' GDP sing 191 n n C4' H4' GDP sing 192 n n O4' C1' GDP sing 193 n n C3' O3' GDP sing 194 n n C3' C2' GDP sing 195 n n C3' H3' GDP sing 196 n n O3' HO3' GDP sing 197 n n C2' O2' GDP sing 198 n n C2' C1' GDP sing 199 n n C2' H2' GDP sing 200 n n O2' HO2' GDP sing 201 n n C1' N9 GDP sing 202 n n C1' H1' GDP sing 203 n n N9 C8 GDP sing 204 n y N9 C4 GDP sing 205 n y C8 N7 GDP doub 206 n y C8 H8 GDP sing 207 n n N7 C5 GDP sing 208 n y C5 C6 GDP sing 209 n n C5 C4 GDP doub 210 n y C6 O6 GDP doub 211 n n C6 N1 GDP sing 212 n n N1 C2 GDP sing 213 n n N1 HN1 GDP sing 214 n n C2 N2 GDP sing 215 n n C2 N3 GDP doub 216 n n N2 HN21 GDP sing 217 n n N2 HN22 GDP sing 218 n n N3 C4 GDP sing 219 n n # _atom_sites.entry_id 5FR2 _atom_sites.fract_transf_matrix[1][1] 0.00565 _atom_sites.fract_transf_matrix[1][2] 0.003262 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006525 _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] 0.01565 _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 3 FAR A 1 1190 1190 FAR FAR . D 4 GDP A 1 1192 1192 GDP GDP . E 5 MG A 1 1193 1193 MG MG . F 6 BGC B 1 1206 1206 BGC BGC . G 7 HOH A 1 2001 2001 HOH HOH . G 7 HOH A 2 2002 2002 HOH HOH . G 7 HOH A 3 2003 2003 HOH HOH . G 7 HOH A 4 2004 2004 HOH HOH . G 7 HOH A 5 2005 2005 HOH HOH . G 7 HOH A 6 2006 2006 HOH HOH . G 7 HOH A 7 2007 2007 HOH HOH . G 7 HOH A 8 2008 2008 HOH HOH . G 7 HOH A 9 2009 2009 HOH HOH . G 7 HOH A 10 2010 2010 HOH HOH . G 7 HOH A 11 2011 2011 HOH HOH . H 7 HOH B 1 2001 2001 HOH HOH . H 7 HOH B 2 2002 2002 HOH HOH . H 7 HOH B 3 2003 2003 HOH HOH . H 7 HOH B 4 2004 2004 HOH HOH . H 7 HOH B 5 2005 2005 HOH HOH . H 7 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 . . . D 4 57.451 -70.788 -14.055 1 44.96 ? PB GDP 1192 A 1 HETATM 2 O O1B GDP . . . D 4 56.884 -69.392 -14.146 1 44.09 ? O1B GDP 1192 A 1 HETATM 3 O O2B GDP . . . D 4 58.32 -70.901 -12.829 1 49.69 ? O2B GDP 1192 A 1 HETATM 4 O O3B GDP . . . D 4 58.248 -71.132 -15.291 1 47.9 ? O3B GDP 1192 A 1 HETATM 5 O O3A GDP . . . D 4 56.233 -71.824 -13.882 1 46.03 ? O3A GDP 1192 A 1 HETATM 6 P PA GDP . . . D 4 55.907 -72.972 -14.962 1 43.44 ? PA GDP 1192 A 1 HETATM 7 O O1A GDP . . . D 4 57.142 -73.782 -15.277 1 45.97 ? O1A GDP 1192 A 1 HETATM 8 O O2A GDP . . . D 4 55.268 -72.413 -16.208 1 40.68 ? O2A GDP 1192 A 1 HETATM 9 O O5' GDP . . . D 4 54.861 -73.872 -14.142 1 43.69 ? O5' GDP 1192 A 1 HETATM 10 C C5' GDP . . . D 4 53.579 -73.351 -13.802 1 45.43 ? C5' GDP 1192 A 1 HETATM 11 C C4' GDP . . . D 4 52.715 -74.447 -13.186 1 52.61 ? C4' GDP 1192 A 1 HETATM 12 O O4' GDP . . . D 4 51.351 -74.074 -13.367 1 57.54 ? O4' GDP 1192 A 1 HETATM 13 C C3' GDP . . . D 4 52.904 -75.78 -13.888 1 55.34 ? C3' GDP 1192 A 1 HETATM 14 O O3' GDP . . . D 4 52.789 -76.861 -12.954 1 54.28 ? O3' GDP 1192 A 1 HETATM 15 C C2' GDP . . . D 4 51.777 -75.845 -14.897 1 60.52 ? C2' GDP 1192 A 1 HETATM 16 O O2' GDP . . . D 4 51.24 -77.168 -14.98 1 66.33 ? O2' GDP 1192 A 1 HETATM 17 C C1' GDP . . . D 4 50.731 -74.87 -14.381 1 60.11 ? C1' GDP 1192 A 1 HETATM 18 N N9 GDP . . . D 4 50.27 -73.984 -15.476 1 57.08 ? N9 GDP 1192 A 1 HETATM 19 C C8 GDP . . . D 4 51.051 -73.35 -16.371 1 52.35 ? C8 GDP 1192 A 1 HETATM 20 N N7 GDP . . . D 4 50.304 -72.611 -17.229 1 52.67 ? N7 GDP 1192 A 1 HETATM 21 C C5 GDP . . . D 4 49.013 -72.762 -16.873 1 56.54 ? C5 GDP 1192 A 1 HETATM 22 C C6 GDP . . . D 4 47.702 -72.263 -17.349 1 58.17 ? C6 GDP 1192 A 1 HETATM 23 O O6 GDP . . . D 4 47.626 -71.492 -18.327 1 59.81 ? O6 GDP 1192 A 1 HETATM 24 N N1 GDP . . . D 4 46.602 -72.661 -16.7 1 57.58 ? N1 GDP 1192 A 1 HETATM 25 C C2 GDP . . . D 4 46.65 -73.49 -15.641 1 57.92 ? C2 GDP 1192 A 1 HETATM 26 N N2 GDP . . . D 4 45.492 -73.848 -15.039 1 58.49 ? N2 GDP 1192 A 1 HETATM 27 N N3 GDP . . . D 4 47.812 -73.988 -15.152 1 59.45 ? N3 GDP 1192 A 1 HETATM 28 C C4 GDP . . . D 4 48.999 -73.664 -15.715 1 58.29 ? C4 GDP 1192 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #