data_3GJ6 # _model_server_result.job_id MQB-4IwAIHajZae-YHN78w _model_server_result.datetime_utc '2024-12-26 15:19:29' _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 3gj6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 3GJ6 # _exptl.entry_id 3GJ6 _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 90 _cell.entry_id 3GJ6 _cell.length_a 60.132 _cell.length_b 80.305 _cell.length_c 54.634 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GJ6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 metalc ? metalc1 A OG1 THR 29 A THR 24 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc2 F O HOH . A HOH 217 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc3 F O HOH . A HOH 218 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc4 F O HOH . A HOH 219 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc5 F O HOH . A HOH 220 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc6 E ZN ZN . B ZN 300 1_555 B SG CYS 12 B CYS 664 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc7 E ZN ZN . B ZN 300 1_555 B SG CYS 15 B CYS 667 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc8 E ZN ZN . B ZN 300 1_555 B SG CYS 26 B CYS 678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 3GJ6 _atom_sites.fract_transf_matrix[1][1] 0.01663 _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] 0.012453 _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] 0.018304 _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 MG A 1 301 301 MG MG . D 4 GDP A 1 302 302 GDP GDP . E 5 ZN B 1 300 300 ZN ZN . F 6 HOH A 1 217 217 HOH HOH . F 6 HOH A 2 218 218 HOH HOH . F 6 HOH A 3 219 219 HOH HOH . F 6 HOH A 4 220 220 HOH HOH . F 6 HOH A 5 221 221 HOH HOH . F 6 HOH A 6 222 222 HOH HOH . F 6 HOH A 7 223 223 HOH HOH . F 6 HOH A 8 224 224 HOH HOH . F 6 HOH A 9 225 225 HOH HOH . F 6 HOH A 10 226 226 HOH HOH . F 6 HOH A 11 227 227 HOH HOH . F 6 HOH A 12 228 228 HOH HOH . F 6 HOH A 13 229 229 HOH HOH . F 6 HOH A 14 230 230 HOH HOH . F 6 HOH A 15 231 231 HOH HOH . F 6 HOH A 16 232 232 HOH HOH . F 6 HOH A 17 233 233 HOH HOH . F 6 HOH A 18 234 234 HOH HOH . F 6 HOH A 19 235 235 HOH HOH . F 6 HOH A 20 236 236 HOH HOH . F 6 HOH A 21 237 237 HOH HOH . F 6 HOH A 22 238 238 HOH HOH . F 6 HOH A 23 240 240 HOH HOH . F 6 HOH A 24 241 241 HOH HOH . F 6 HOH A 25 242 242 HOH HOH . F 6 HOH A 26 243 243 HOH HOH . F 6 HOH A 27 244 244 HOH HOH . F 6 HOH A 28 245 245 HOH HOH . F 6 HOH A 29 246 246 HOH HOH . F 6 HOH A 30 247 247 HOH HOH . F 6 HOH A 31 248 248 HOH HOH . F 6 HOH A 32 249 249 HOH HOH . F 6 HOH A 33 250 250 HOH HOH . G 6 HOH B 1 7 7 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 9.066 18.184 -8.176 1 50.54 ? PB GDP 302 A 1 HETATM 2 O O1B GDP . . . D 4 8.896 19.296 -7.181 1 52.78 ? O1B GDP 302 A 1 HETATM 3 O O2B GDP . . . D 4 9.937 17.121 -7.549 1 50.91 ? O2B GDP 302 A 1 HETATM 4 O O3B GDP . . . D 4 7.701 17.66 -8.538 1 47.76 ? O3B GDP 302 A 1 HETATM 5 O O3A GDP . . . D 4 9.776 18.646 -9.552 1 52.06 ? O3A GDP 302 A 1 HETATM 6 P PA GDP . . . D 4 10.676 19.983 -9.736 1 52.23 ? PA GDP 302 A 1 HETATM 7 O O1A GDP . . . D 4 9.824 21.23 -9.672 1 62.61 ? O1A GDP 302 A 1 HETATM 8 O O2A GDP . . . D 4 11.812 20.07 -8.752 1 48.07 ? O2A GDP 302 A 1 HETATM 9 O O5' GDP . . . D 4 11.227 19.735 -11.219 1 76.97 ? O5' GDP 302 A 1 HETATM 10 C C5' GDP . . . D 4 12.1 18.629 -11.428 1 72.68 ? C5' GDP 302 A 1 HETATM 11 C C4' GDP . . . D 4 12.76 18.809 -12.779 1 69.38 ? C4' GDP 302 A 1 HETATM 12 O O4' GDP . . . D 4 11.724 18.954 -13.75 1 70.04 ? O4' GDP 302 A 1 HETATM 13 C C3' GDP . . . D 4 13.58 20.094 -12.775 1 72.42 ? C3' GDP 302 A 1 HETATM 14 O O3' GDP . . . D 4 14.918 19.869 -13.271 1 64.01 ? O3' GDP 302 A 1 HETATM 15 C C2' GDP . . . D 4 12.774 21.058 -13.641 1 70.73 ? C2' GDP 302 A 1 HETATM 16 O O2' GDP . . . D 4 13.579 21.986 -14.39 1 72.55 ? O2' GDP 302 A 1 HETATM 17 C C1' GDP . . . D 4 11.953 20.132 -14.531 1 68.97 ? C1' GDP 302 A 1 HETATM 18 N N9 GDP . . . D 4 10.679 20.775 -14.932 1 64.95 ? N9 GDP 302 A 1 HETATM 19 C C8 GDP . . . D 4 9.704 21.188 -14.101 1 59.12 ? C8 GDP 302 A 1 HETATM 20 N N7 GDP . . . D 4 8.677 21.733 -14.801 1 61.6 ? N7 GDP 302 A 1 HETATM 21 C C5 GDP . . . D 4 8.994 21.669 -16.106 1 62.18 ? C5 GDP 302 A 1 HETATM 22 C C6 GDP . . . D 4 8.356 22.068 -17.383 1 61.85 ? C6 GDP 302 A 1 HETATM 23 O O6 GDP . . . D 4 7.237 22.622 -17.404 1 55.2 ? O6 GDP 302 A 1 HETATM 24 N N1 GDP . . . D 4 9.018 21.825 -18.523 1 66.39 ? N1 GDP 302 A 1 HETATM 25 C C2 GDP . . . D 4 10.234 21.248 -18.547 1 65.72 ? C2 GDP 302 A 1 HETATM 26 N N2 GDP . . . D 4 10.827 21.05 -19.75 1 65.55 ? N2 GDP 302 A 1 HETATM 27 N N3 GDP . . . D 4 10.878 20.856 -17.412 1 67.12 ? N3 GDP 302 A 1 HETATM 28 C C4 GDP . . . D 4 10.317 21.037 -16.189 1 64.21 ? C4 GDP 302 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 28 #