data_5FR1 # _model_server_result.job_id 9UYhRIUogHs8kW9SH5AJGw _model_server_result.datetime_utc '2024-11-14 21:56:22' _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 5fr1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1194}' # _entry.id 5FR1 # _exptl.entry_id 5FR1 _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 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 5FR1 _cell.length_a 53.1 _cell.length_b 67.64 _cell.length_c 120.23 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5FR1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 3 _struct_asym.id C _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 B C MET 135 B MET 126 1_555 B N ALY 136 B ALY 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale2 B C ALY 136 B ALY 127 1_555 B N TYR 137 B TYR 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C ASP 149 B ASP 140 1_555 B N ALY 150 B ALY 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale4 B C ALY 150 B ALY 141 1_555 B N THR 151 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? metalc ? metalc1 A OG1 THR 22 A THR 19 1_555 D MG MG . A MG 1195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 A O THR 40 A THR 37 1_555 D MG MG . A MG 1195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc3 C O1B GDP . A GDP 1194 1_555 D MG MG . A MG 1195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc4 C O3B GDP . A GDP 1194 1_555 D MG MG . A MG 1195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc5 D MG MG . A MG 1195 1_555 G O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc6 D MG MG . A MG 1195 1_555 G O HOH . A HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? metalc ? metalc7 B O ARG 161 B ARG 152 1_555 F MG MG . B MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? # _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 111 n n PB O2B GDP sing 112 n n PB O3B GDP sing 113 n n PB O3A GDP sing 114 n n O2B HOB2 GDP sing 115 n n O3B HOB3 GDP sing 116 n n O3A PA GDP sing 117 n n PA O1A GDP doub 118 n n PA O2A GDP sing 119 n n PA O5' GDP sing 120 n n O2A HOA2 GDP sing 121 n n O5' C5' GDP sing 122 n n C5' C4' GDP sing 123 n n C5' H5' GDP sing 124 n n C5' "H5''" GDP sing 125 n n C4' O4' GDP sing 126 n n C4' C3' GDP sing 127 n n C4' H4' GDP sing 128 n n O4' C1' GDP sing 129 n n C3' O3' GDP sing 130 n n C3' C2' GDP sing 131 n n C3' H3' GDP sing 132 n n O3' HO3' GDP sing 133 n n C2' O2' GDP sing 134 n n C2' C1' GDP sing 135 n n C2' H2' GDP sing 136 n n O2' HO2' GDP sing 137 n n C1' N9 GDP sing 138 n n C1' H1' GDP sing 139 n n N9 C8 GDP sing 140 n y N9 C4 GDP sing 141 n y C8 N7 GDP doub 142 n y C8 H8 GDP sing 143 n n N7 C5 GDP sing 144 n y C5 C6 GDP sing 145 n n C5 C4 GDP doub 146 n y C6 O6 GDP doub 147 n n C6 N1 GDP sing 148 n n N1 C2 GDP sing 149 n n N1 HN1 GDP sing 150 n n C2 N2 GDP sing 151 n n C2 N3 GDP doub 152 n n N2 HN21 GDP sing 153 n n N2 HN22 GDP sing 154 n n N3 C4 GDP sing 155 n n # _atom_sites.entry_id 5FR1 _atom_sites.fract_transf_matrix[1][1] 0.018832 _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] 0.014784 _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] 0.008317 _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 GDP A 1 1194 1194 GDP GDP . D 4 MG A 1 1195 1195 MG MG . E 4 MG A 1 1196 1196 MG MG . F 4 MG B 1 1203 1203 MG MG . G 5 HOH A 1 2001 2001 HOH HOH . G 5 HOH A 2 2002 2002 HOH HOH . G 5 HOH A 3 2003 2003 HOH HOH . G 5 HOH A 4 2004 2004 HOH HOH . G 5 HOH A 5 2005 2005 HOH HOH . G 5 HOH A 6 2006 2006 HOH HOH . G 5 HOH A 7 2007 2007 HOH HOH . G 5 HOH A 8 2008 2008 HOH HOH . G 5 HOH A 9 2009 2009 HOH HOH . G 5 HOH A 10 2010 2010 HOH HOH . H 5 HOH B 1 2001 2001 HOH HOH . H 5 HOH B 2 2002 2002 HOH HOH . H 5 HOH B 3 2003 2003 HOH HOH . H 5 HOH B 4 2004 2004 HOH HOH . H 5 HOH B 5 2005 2005 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 3 -11.752 17.513 -17.684 1 51.21 ? PB GDP 1194 A 1 HETATM 2 O O1B GDP . . . C 3 -12.795 16.507 -17.545 1 55.4 ? O1B GDP 1194 A 1 HETATM 3 O O2B GDP . . . C 3 -10.46 16.96 -17.85 1 50.83 ? O2B GDP 1194 A 1 HETATM 4 O O3B GDP . . . C 3 -11.755 18.585 -16.686 1 50.8 ? O3B GDP 1194 A 1 HETATM 5 O O3A GDP . . . C 3 -12.162 18.184 -19.08 1 54.3 ? O3A GDP 1194 A 1 HETATM 6 P PA GDP . . . C 3 -13.686 18.502 -19.686 1 57.11 ? PA GDP 1194 A 1 HETATM 7 O O1A GDP . . . C 3 -14.563 19.279 -18.799 1 54.1 ? O1A GDP 1194 A 1 HETATM 8 O O2A GDP . . . C 3 -14.277 17.353 -20.383 1 60.92 ? O2A GDP 1194 A 1 HETATM 9 O O5' GDP . . . C 3 -13.259 19.417 -20.817 1 58.43 ? O5' GDP 1194 A 1 HETATM 10 C C5' GDP . . . C 3 -12.499 20.629 -20.598 1 58.43 ? C5' GDP 1194 A 1 HETATM 11 C C4' GDP . . . C 3 -12.679 21.65 -21.747 1 56.45 ? C4' GDP 1194 A 1 HETATM 12 O O4' GDP . . . C 3 -12.133 21.185 -22.995 1 58.42 ? O4' GDP 1194 A 1 HETATM 13 C C3' GDP . . . C 3 -14.147 21.913 -21.987 1 58.46 ? C3' GDP 1194 A 1 HETATM 14 O O3' GDP . . . C 3 -14.443 23.258 -22.299 1 59.4 ? O3' GDP 1194 A 1 HETATM 15 C C2' GDP . . . C 3 -14.458 21.047 -23.163 1 59.83 ? C2' GDP 1194 A 1 HETATM 16 O O2' GDP . . . C 3 -15.453 21.63 -23.934 1 60.68 ? O2' GDP 1194 A 1 HETATM 17 C C1' GDP . . . C 3 -13.209 21.032 -23.951 1 59.55 ? C1' GDP 1194 A 1 HETATM 18 N N9 GDP . . . C 3 -13.107 19.767 -24.712 1 62.8 ? N9 GDP 1194 A 1 HETATM 19 C C8 GDP . . . C 3 -13.282 18.512 -24.319 1 62.56 ? C8 GDP 1194 A 1 HETATM 20 N N7 GDP . . . C 3 -13.1 17.726 -25.365 1 62.21 ? N7 GDP 1194 A 1 HETATM 21 C C5 GDP . . . C 3 -12.817 18.47 -26.408 1 64.07 ? C5 GDP 1194 A 1 HETATM 22 C C6 GDP . . . C 3 -12.537 18.15 -27.664 1 64.53 ? C6 GDP 1194 A 1 HETATM 23 O O6 GDP . . . C 3 -12.512 16.972 -28.024 1 61.84 ? O6 GDP 1194 A 1 HETATM 24 N N1 GDP . . . C 3 -12.262 19.195 -28.565 1 67.23 ? N1 GDP 1194 A 1 HETATM 25 C C2 GDP . . . C 3 -12.283 20.519 -28.127 1 64.85 ? C2 GDP 1194 A 1 HETATM 26 N N2 GDP . . . C 3 -12.023 21.502 -28.949 1 64.13 ? N2 GDP 1194 A 1 HETATM 27 N N3 GDP . . . C 3 -12.557 20.772 -26.849 1 66.57 ? N3 GDP 1194 A 1 HETATM 28 C C4 GDP . . . C 3 -12.821 19.749 -26.003 1 66.57 ? C4 GDP 1194 A 1 HETATM 29 H H5' GDP . . . C 3 -12.775 21.035 -19.761 1 58.43 ? H5' GDP 1194 A 1 HETATM 30 H "H5''" GDP . . . C 3 -11.559 20.407 -20.509 1 58.43 ? "H5''" GDP 1194 A 1 HETATM 31 H H4' GDP . . . C 3 -12.208 22.45 -21.467 1 56.45 ? H4' GDP 1194 A 1 HETATM 32 H H3' GDP . . . C 3 -14.667 21.727 -21.19 1 58.46 ? H3' GDP 1194 A 1 HETATM 33 H HO3' GDP . . . C 3 -13.841 23.57 -22.795 1 59.4 ? HO3' GDP 1194 A 1 HETATM 34 H H2' GDP . . . C 3 -14.758 20.165 -22.894 1 59.83 ? H2' GDP 1194 A 1 HETATM 35 H HO2' GDP . . . C 3 -15.267 22.438 -24.068 1 60.68 ? HO2' GDP 1194 A 1 HETATM 36 H H1' GDP . . . C 3 -13.177 21.746 -24.607 1 59.55 ? H1' GDP 1194 A 1 HETATM 37 H H8 GDP . . . C 3 -13.505 18.222 -23.42 1 62.56 ? H8 GDP 1194 A 1 HETATM 38 H HN1 GDP . . . C 3 -12.081 19.017 -29.387 1 67.23 ? HN1 GDP 1194 A 1 HETATM 39 H HN21 GDP . . . C 3 -12.039 22.314 -28.667 1 64.13 ? HN21 GDP 1194 A 1 HETATM 40 H HN22 GDP . . . C 3 -11.836 21.336 -29.772 1 64.13 ? HN22 GDP 1194 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #