data_3T1O # _model_server_result.job_id XvG7tbp_P2YVxbhEl5PCtA _model_server_result.datetime_utc '2024-11-08 13:44:31' _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 3t1o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":274}' # _entry.id 3T1O # _exptl.entry_id 3T1O _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 108.37 _cell.angle_beta 100.1 _cell.angle_gamma 92.92 _cell.entry_id 3T1O _cell.length_a 45.3 _cell.length_b 47.85 _cell.length_c 53.08 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3T1O _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,L 1 1 B,I,J,K,M 2 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 I 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 metalc ? metalc1 A O GLU 45 A GLU 43 1_555 H MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc2 A OD1 ASP 60 A ASP 58 1_555 H MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc3 A O VAL 81 A VAL 79 1_555 E MG MG . A MG 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc4 A O GLY 83 A GLY 81 1_555 E MG MG . A MG 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc5 A O ASP 106 A ASP 104 1_555 F MG MG . A MG 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc6 A O ALA 108 A ALA 106 1_555 F MG MG . A MG 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc7 A O ARG 123 A ARG 121 1_555 G MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc8 A O LEU 131 A LEU 129 1_555 G MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? metalc ? metalc9 E MG MG . A MG 197 1_555 L O HOH . A HOH 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? metalc ? metalc10 B O VAL 81 B VAL 79 1_555 J MG MG . B MG 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc11 B O GLY 83 B GLY 81 1_555 J MG MG . B MG 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? # _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 3T1O _atom_sites.fract_transf_matrix[1][1] 0.022075 _atom_sites.fract_transf_matrix[1][2] 0.001126 _atom_sites.fract_transf_matrix[1][3] 0.004558 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020926 _atom_sites.fract_transf_matrix[2][3] 0.007306 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.020269 _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 1 274 274 GDP GDP . D 3 MPD A 1 5276 5276 MPD MPD . E 4 MG A 1 197 197 MG MG . F 4 MG A 1 198 198 MG MG . G 4 MG A 1 199 199 MG MG . H 4 MG A 1 200 200 MG MG . I 2 GDP B 1 274 274 GDP GDP . J 4 MG B 1 197 197 MG MG . K 4 MG B 1 198 198 MG MG . L 5 HOH A 1 201 201 HOH HOH . L 5 HOH A 2 202 202 HOH HOH . L 5 HOH A 3 203 203 HOH HOH . L 5 HOH A 4 204 204 HOH HOH . L 5 HOH A 5 205 205 HOH HOH . L 5 HOH A 6 206 206 HOH HOH . L 5 HOH A 7 207 207 HOH HOH . L 5 HOH A 8 208 208 HOH HOH . L 5 HOH A 9 209 209 HOH HOH . L 5 HOH A 10 210 210 HOH HOH . L 5 HOH A 11 211 211 HOH HOH . L 5 HOH A 12 212 212 HOH HOH . L 5 HOH A 13 213 213 HOH HOH . L 5 HOH A 14 214 214 HOH HOH . L 5 HOH A 15 215 215 HOH HOH . L 5 HOH A 16 216 216 HOH HOH . L 5 HOH A 17 218 218 HOH HOH . L 5 HOH A 18 219 219 HOH HOH . L 5 HOH A 19 221 221 HOH HOH . L 5 HOH A 20 222 222 HOH HOH . L 5 HOH A 21 223 223 HOH HOH . L 5 HOH A 22 224 224 HOH HOH . L 5 HOH A 23 225 225 HOH HOH . L 5 HOH A 24 226 226 HOH HOH . L 5 HOH A 25 227 227 HOH HOH . L 5 HOH A 26 228 228 HOH HOH . L 5 HOH A 27 229 229 HOH HOH . L 5 HOH A 28 230 230 HOH HOH . L 5 HOH A 29 231 231 HOH HOH . L 5 HOH A 30 232 232 HOH HOH . L 5 HOH A 31 233 233 HOH HOH . L 5 HOH A 32 234 234 HOH HOH . L 5 HOH A 33 235 235 HOH HOH . L 5 HOH A 34 236 236 HOH HOH . L 5 HOH A 35 237 237 HOH HOH . L 5 HOH A 36 238 238 HOH HOH . L 5 HOH A 37 239 239 HOH HOH . L 5 HOH A 38 240 240 HOH HOH . L 5 HOH A 39 241 241 HOH HOH . L 5 HOH A 40 242 242 HOH HOH . L 5 HOH A 41 243 243 HOH HOH . L 5 HOH A 42 244 244 HOH HOH . L 5 HOH A 43 245 245 HOH HOH . L 5 HOH A 44 247 247 HOH HOH . L 5 HOH A 45 250 250 HOH HOH . L 5 HOH A 46 251 251 HOH HOH . M 5 HOH B 1 199 199 HOH HOH . M 5 HOH B 2 200 200 HOH HOH . M 5 HOH B 3 201 201 HOH HOH . M 5 HOH B 4 202 202 HOH HOH . M 5 HOH B 5 203 203 HOH HOH . M 5 HOH B 6 204 204 HOH HOH . M 5 HOH B 7 205 205 HOH HOH . M 5 HOH B 8 206 206 HOH HOH . M 5 HOH B 9 207 207 HOH HOH . M 5 HOH B 10 208 208 HOH HOH . M 5 HOH B 11 209 209 HOH HOH . M 5 HOH B 12 210 210 HOH HOH . M 5 HOH B 13 211 211 HOH HOH . M 5 HOH B 14 212 212 HOH HOH . M 5 HOH B 15 213 213 HOH HOH . M 5 HOH B 16 214 214 HOH HOH . M 5 HOH B 17 215 215 HOH HOH . M 5 HOH B 18 216 216 HOH HOH . M 5 HOH B 19 217 217 HOH HOH . M 5 HOH B 20 218 218 HOH HOH . M 5 HOH B 21 219 219 HOH HOH . M 5 HOH B 22 220 220 HOH HOH . M 5 HOH B 23 221 221 HOH HOH . M 5 HOH B 24 222 222 HOH HOH . M 5 HOH B 25 223 223 HOH HOH . M 5 HOH B 26 224 224 HOH HOH . M 5 HOH B 27 225 225 HOH HOH . M 5 HOH B 28 226 226 HOH HOH . M 5 HOH B 29 227 227 HOH HOH . M 5 HOH B 30 228 228 HOH HOH . M 5 HOH B 31 229 229 HOH HOH . M 5 HOH B 32 230 230 HOH HOH . M 5 HOH B 33 231 231 HOH HOH . M 5 HOH B 34 232 232 HOH HOH . M 5 HOH B 35 233 233 HOH HOH . M 5 HOH B 36 234 234 HOH HOH . M 5 HOH B 37 235 235 HOH HOH . M 5 HOH B 38 236 236 HOH HOH . M 5 HOH B 39 237 237 HOH HOH . M 5 HOH B 40 238 238 HOH HOH . M 5 HOH B 41 239 239 HOH HOH . M 5 HOH B 42 240 240 HOH HOH . M 5 HOH B 43 241 241 HOH HOH . M 5 HOH B 44 242 242 HOH HOH . M 5 HOH B 45 243 243 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 7.516 5.56 21.363 1 20.38 ? PB GDP 274 A 1 HETATM 2 O O1B GDP . . . C 2 6.34 5.289 20.436 1 17.55 ? O1B GDP 274 A 1 HETATM 3 O O2B GDP . . . C 2 6.934 6.296 22.52 1 19.87 ? O2B GDP 274 A 1 HETATM 4 O O3B GDP . . . C 2 8.597 6.286 20.683 1 21.05 ? O3B GDP 274 A 1 HETATM 5 O O3A GDP . . . C 2 7.964 4.09 21.911 1 17.59 ? O3A GDP 274 A 1 HETATM 6 P PA GDP . . . C 2 9.295 3.271 21.718 1 18.24 ? PA GDP 274 A 1 HETATM 7 O O1A GDP . . . C 2 10.286 3.919 22.571 1 13.83 ? O1A GDP 274 A 1 HETATM 8 O O2A GDP . . . C 2 9.708 3.112 20.314 1 20.81 ? O2A GDP 274 A 1 HETATM 9 O O5' GDP . . . C 2 8.836 1.793 22.294 1 17.44 ? O5' GDP 274 A 1 HETATM 10 C C5' GDP . . . C 2 8.315 1.713 23.606 1 23 ? C5' GDP 274 A 1 HETATM 11 C C4' GDP . . . C 2 8.78 0.387 24.254 1 19.34 ? C4' GDP 274 A 1 HETATM 12 O O4' GDP . . . C 2 8.24 -0.564 23.417 1 18.27 ? O4' GDP 274 A 1 HETATM 13 C C3' GDP . . . C 2 10.289 0.125 24.181 1 27.08 ? C3' GDP 274 A 1 HETATM 14 O O3' GDP . . . C 2 10.605 -0.554 25.39 1 32.43 ? O3' GDP 274 A 1 HETATM 15 C C2' GDP . . . C 2 10.485 -0.778 22.976 1 25.4 ? C2' GDP 274 A 1 HETATM 16 O O2' GDP . . . C 2 11.554 -1.747 23.079 1 29.65 ? O2' GDP 274 A 1 HETATM 17 C C1' GDP . . . C 2 9.186 -1.5 22.938 1 23.37 ? C1' GDP 274 A 1 HETATM 18 N N9 GDP . . . C 2 8.845 -1.958 21.547 1 24.37 ? N9 GDP 274 A 1 HETATM 19 C C8 GDP . . . C 2 8.865 -1.257 20.383 1 15.72 ? C8 GDP 274 A 1 HETATM 20 N N7 GDP . . . C 2 8.503 -2.033 19.342 1 18.58 ? N7 GDP 274 A 1 HETATM 21 C C5 GDP . . . C 2 8.249 -3.252 19.878 1 18.79 ? C5 GDP 274 A 1 HETATM 22 C C6 GDP . . . C 2 7.825 -4.541 19.366 1 22.3 ? C6 GDP 274 A 1 HETATM 23 O O6 GDP . . . C 2 7.617 -4.682 18.163 1 20.97 ? O6 GDP 274 A 1 HETATM 24 N N1 GDP . . . C 2 7.651 -5.585 20.224 1 23.17 ? N1 GDP 274 A 1 HETATM 25 C C2 GDP . . . C 2 7.896 -5.44 21.561 1 24.9 ? C2 GDP 274 A 1 HETATM 26 N N2 GDP . . . C 2 7.731 -6.487 22.429 1 26.02 ? N2 GDP 274 A 1 HETATM 27 N N3 GDP . . . C 2 8.304 -4.307 22.092 1 23.52 ? N3 GDP 274 A 1 HETATM 28 C C4 GDP . . . C 2 8.444 -3.196 21.31 1 22.36 ? C4 GDP 274 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 28 #