data_1TL7 # _model_server_result.job_id fX_HYD0Izv7dclnW-4FNyw _model_server_result.datetime_utc '2024-10-26 22:28:25' _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 1tl7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":405}' # _entry.id 1TL7 # _exptl.entry_id 1TL7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 1TL7 _cell.length_a 118.23 _cell.length_b 133.6 _cell.length_c 70.35 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TL7 _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 PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,I,J,K,L,M _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 9 _struct_asym.id J _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 G O2A ONM . A ONM 100 1_555 D MN MN . A MN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? metalc ? metalc2 G O3B ONM . A ONM 100 1_555 D MN MN . A MN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc3 G O1B ONM . A ONM 100 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc4 G O3B ONM . A ONM 100 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc5 A OD1 ASP 33 A ASP 396 1_555 D MN MN . A MN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? metalc ? metalc6 A OD2 ASP 33 A ASP 396 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc7 A O ILE 34 A ILE 397 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc8 A OD1 ASP 77 A ASP 440 1_555 D MN MN . A MN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc9 A OD2 ASP 77 A ASP 440 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc10 C OG SER 54 C SER 54 1_555 H MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc11 C OG1 THR 204 C THR 204 1_555 H MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc12 H MG MG . C MG 403 1_555 J O3G GSP . C GSP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc13 H MG MG . C MG 403 1_555 J O2G GSP . C GSP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc14 H MG MG . C MG 403 1_555 J O2B GSP . C GSP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc15 H MG MG . C MG 403 1_555 M O HOH . C HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _chem_comp.type non-polymer _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 PG O3B GSP sing 194 n n PG S1G GSP doub 195 n n PG O2G GSP sing 196 n n PG O3G GSP sing 197 n n O3B PB GSP sing 198 n n O2G HOG2 GSP sing 199 n n O3G HOG3 GSP sing 200 n n PB O1B GSP doub 201 n n PB O2B GSP sing 202 n n PB O3A GSP sing 203 n n O2B HOB2 GSP sing 204 n n PA O1A GSP doub 205 n n PA O2A GSP sing 206 n n PA O3A GSP sing 207 n n PA O5' GSP sing 208 n n O2A HOA2 GSP sing 209 n n O5' C5' GSP sing 210 n n C5' C4' GSP sing 211 n n C5' "H5'1" GSP sing 212 n n C5' "H5'2" GSP sing 213 n n C4' O4' GSP sing 214 n n C4' C3' GSP sing 215 n n C4' H4' GSP sing 216 n n O4' C1' GSP sing 217 n n C3' O3' GSP sing 218 n n C3' C2' GSP sing 219 n n C3' H3' GSP sing 220 n n O3' HO3' GSP sing 221 n n C2' O2' GSP sing 222 n n C2' C1' GSP sing 223 n n C2' H2' GSP sing 224 n n O2' HO2' GSP sing 225 n n C1' N9 GSP sing 226 n n C1' H1' GSP sing 227 n n N9 C8 GSP sing 228 n y N9 C4 GSP sing 229 n y C8 N7 GSP doub 230 n y C8 H8 GSP sing 231 n n N7 C5 GSP sing 232 n y C5 C6 GSP sing 233 n n C5 C4 GSP doub 234 n y C6 O6 GSP doub 235 n n C6 N1 GSP sing 236 n n N1 C2 GSP sing 237 n n N1 HN1 GSP sing 238 n n C2 N2 GSP sing 239 n n C2 N3 GSP doub 240 n n N2 HN21 GSP sing 241 n n N2 HN22 GSP sing 242 n n N3 C4 GSP sing 243 n n # _atom_sites.entry_id 1TL7 _atom_sites.fract_transf_matrix[1][1] 0.008458 _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] 0.007485 _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] 0.014215 _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 D 4 MN A 1 581 502 MN MN . E 4 MN A 1 582 503 MN MN . F 5 FOK A 1 101 101 FOK FOK . G 6 ONM A 1 100 100 ONM ONM . H 7 MG C 1 403 396 MG MG . I 8 CL C 1 404 397 CL CL . J 9 GSP C 1 405 395 GSP GSP . K 10 HOH A 1 22 22 HOH HOH . L 10 HOH B 1 13 13 HOH HOH . L 10 HOH B 2 14 14 HOH HOH . L 10 HOH B 3 15 15 HOH HOH . L 10 HOH B 4 24 24 HOH HOH . L 10 HOH B 5 26 26 HOH HOH . L 10 HOH B 6 28 28 HOH HOH . L 10 HOH B 7 29 29 HOH HOH . L 10 HOH B 8 37 37 HOH HOH . L 10 HOH B 9 52 52 HOH HOH . M 10 HOH C 1 406 2 HOH HOH . M 10 HOH C 2 407 3 HOH HOH . M 10 HOH C 3 408 38 HOH HOH . M 10 HOH C 4 409 41 HOH HOH . M 10 HOH C 5 410 43 HOH HOH . M 10 HOH C 6 411 51 HOH HOH . M 10 HOH C 7 412 10 HOH HOH . M 10 HOH C 8 413 40 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 PG GSP . . . J 9 23.44 3.813 28.605 1 60.28 ? PG GSP 405 C 1 HETATM 2 O O3B GSP . . . J 9 22.661 3.477 27.202 1 47.55 ? O3B GSP 405 C 1 HETATM 3 S S1G GSP . . . J 9 25.046 4.559 27.978 1 66.23 ? S1G GSP 405 C 1 HETATM 4 O O2G GSP . . . J 9 22.393 4.628 29.271 1 58.84 ? O2G GSP 405 C 1 HETATM 5 O O3G GSP . . . J 9 23.961 2.572 29.26 1 56.68 ? O3G GSP 405 C 1 HETATM 6 P PB GSP . . . J 9 21.148 2.791 27.136 1 31.64 ? PB GSP 405 C 1 HETATM 7 O O1B GSP . . . J 9 21.445 1.613 26.347 1 31.65 ? O1B GSP 405 C 1 HETATM 8 O O2B GSP . . . J 9 20.427 2.492 28.402 1 29.58 ? O2B GSP 405 C 1 HETATM 9 P PA GSP . . . J 9 18.948 4.528 27 1 26.57 ? PA GSP 405 C 1 HETATM 10 O O1A GSP . . . J 9 17.931 3.502 27.324 1 33.61 ? O1A GSP 405 C 1 HETATM 11 O O2A GSP . . . J 9 19.463 5.474 28.025 1 28.26 ? O2A GSP 405 C 1 HETATM 12 O O3A GSP . . . J 9 20.194 3.84 26.355 1 30.03 ? O3A GSP 405 C 1 HETATM 13 O O5' GSP . . . J 9 18.341 5.458 25.78 1 23.76 ? O5' GSP 405 C 1 HETATM 14 C C5' GSP . . . J 9 19.076 6.587 25.2 1 27.37 ? C5' GSP 405 C 1 HETATM 15 C C4' GSP . . . J 9 18.075 7.471 24.476 1 29.27 ? C4' GSP 405 C 1 HETATM 16 O O4' GSP . . . J 9 17.396 6.703 23.414 1 27.08 ? O4' GSP 405 C 1 HETATM 17 C C3' GSP . . . J 9 16.895 7.982 25.387 1 29.8 ? C3' GSP 405 C 1 HETATM 18 O O3' GSP . . . J 9 16.756 9.408 25.144 1 30.51 ? O3' GSP 405 C 1 HETATM 19 C C2' GSP . . . J 9 15.631 7.187 24.847 1 30.27 ? C2' GSP 405 C 1 HETATM 20 O O2' GSP . . . J 9 14.39 7.895 25.023 1 39.06 ? O2' GSP 405 C 1 HETATM 21 C C1' GSP . . . J 9 15.982 6.991 23.35 1 28.02 ? C1' GSP 405 C 1 HETATM 22 N N9 GSP . . . J 9 15.372 5.788 22.707 1 26.81 ? N9 GSP 405 C 1 HETATM 23 C C8 GSP . . . J 9 15.298 4.462 23.069 1 24.04 ? C8 GSP 405 C 1 HETATM 24 N N7 GSP . . . J 9 14.675 3.681 22.241 1 23.69 ? N7 GSP 405 C 1 HETATM 25 C C5 GSP . . . J 9 14.291 4.553 21.226 1 23.71 ? C5 GSP 405 C 1 HETATM 26 C C6 GSP . . . J 9 13.555 4.248 20.017 1 25.35 ? C6 GSP 405 C 1 HETATM 27 O O6 GSP . . . J 9 13.171 3.118 19.743 1 24.63 ? O6 GSP 405 C 1 HETATM 28 N N1 GSP . . . J 9 13.372 5.411 19.259 1 27.55 ? N1 GSP 405 C 1 HETATM 29 C C2 GSP . . . J 9 13.816 6.71 19.579 1 28.62 ? C2 GSP 405 C 1 HETATM 30 N N2 GSP . . . J 9 13.565 7.728 18.758 1 25.86 ? N2 GSP 405 C 1 HETATM 31 N N3 GSP . . . J 9 14.513 6.976 20.73 1 25.31 ? N3 GSP 405 C 1 HETATM 32 C C4 GSP . . . J 9 14.711 5.846 21.503 1 23.69 ? C4 GSP 405 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #