data_2GVD # _model_server_result.job_id 0DvhjIRUn90sFUTdqS3SkQ _model_server_result.datetime_utc '2024-11-22 05:48:46' _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 2gvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":395}' # _entry.id 2GVD # _exptl.entry_id 2GVD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 8 _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 2GVD _cell.length_a 118.2 _cell.length_b 133.4 _cell.length_c 70.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GVD _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,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 8 _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 disulf ? disulf1 A SG CYS 77 A CYS 432 1_555 A SG CYS 89 A CYS 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc1 A OD2 ASP 41 A ASP 396 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc2 A OD1 ASP 41 A ASP 396 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc3 A O ILE 42 A ILE 397 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc4 A OD1 ASP 85 A ASP 440 1_555 D MN MN . A MN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc5 A OD2 ASP 85 A ASP 440 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc6 E MN MN . A MN 582 1_555 G O2B 128 . A 128 584 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc7 E MN MN . A MN 582 1_555 G O3B 128 . A 128 584 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc8 C OG SER 54 C SER 54 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc9 C OG1 THR 204 C THR 204 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc10 J O2B GSP . C GSP 395 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc11 J O2G GSP . C GSP 395 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? # _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 288 n n PG S1G GSP doub 289 n n PG O2G GSP sing 290 n n PG O3G GSP sing 291 n n O3B PB GSP sing 292 n n O2G HOG2 GSP sing 293 n n O3G HOG3 GSP sing 294 n n PB O1B GSP doub 295 n n PB O2B GSP sing 296 n n PB O3A GSP sing 297 n n O2B HOB2 GSP sing 298 n n PA O1A GSP doub 299 n n PA O2A GSP sing 300 n n PA O3A GSP sing 301 n n PA O5' GSP sing 302 n n O2A HOA2 GSP sing 303 n n O5' C5' GSP sing 304 n n C5' C4' GSP sing 305 n n C5' "H5'1" GSP sing 306 n n C5' "H5'2" GSP sing 307 n n C4' O4' GSP sing 308 n n C4' C3' GSP sing 309 n n C4' H4' GSP sing 310 n n O4' C1' GSP sing 311 n n C3' O3' GSP sing 312 n n C3' C2' GSP sing 313 n n C3' H3' GSP sing 314 n n O3' HO3' GSP sing 315 n n C2' O2' GSP sing 316 n n C2' C1' GSP sing 317 n n C2' H2' GSP sing 318 n n O2' HO2' GSP sing 319 n n C1' N9 GSP sing 320 n n C1' H1' GSP sing 321 n n N9 C8 GSP sing 322 n y N9 C4 GSP sing 323 n y C8 N7 GSP doub 324 n y C8 H8 GSP sing 325 n n N7 C5 GSP sing 326 n y C5 C6 GSP sing 327 n n C5 C4 GSP doub 328 n y C6 O6 GSP doub 329 n n C6 N1 GSP sing 330 n n N1 C2 GSP sing 331 n n N1 HN1 GSP sing 332 n n C2 N2 GSP sing 333 n n C2 N3 GSP doub 334 n n N2 HN21 GSP sing 335 n n N2 HN22 GSP sing 336 n n N3 C4 GSP sing 337 n n # _atom_sites.entry_id 2GVD _atom_sites.fract_transf_matrix[1][1] 0.00846 _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] 0.007496 _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] 0.014164 _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 FKP A 1 583 1 FKP FKP . G 6 128 A 1 584 10 128 128 . H 4 MN C 1 396 396 MN MN . I 7 CL C 1 397 397 CL CL . J 8 GSP C 1 395 395 GSP GSP . K 9 HOH A 1 1 1 HOH HOH . K 9 HOH A 2 11 11 HOH HOH . K 9 HOH A 3 19 19 HOH HOH . K 9 HOH A 4 21 21 HOH HOH . K 9 HOH A 5 23 23 HOH HOH . K 9 HOH A 6 31 31 HOH HOH . K 9 HOH A 7 42 42 HOH HOH . K 9 HOH A 8 45 45 HOH HOH . K 9 HOH A 9 56 56 HOH HOH . K 9 HOH A 10 63 63 HOH HOH . K 9 HOH A 11 68 68 HOH HOH . L 9 HOH B 1 2 2 HOH HOH . L 9 HOH B 2 4 4 HOH HOH . L 9 HOH B 3 5 5 HOH HOH . L 9 HOH B 4 7 7 HOH HOH . L 9 HOH B 5 9 9 HOH HOH . L 9 HOH B 6 10 10 HOH HOH . L 9 HOH B 7 12 12 HOH HOH . L 9 HOH B 8 13 13 HOH HOH . L 9 HOH B 9 15 15 HOH HOH . L 9 HOH B 10 16 16 HOH HOH . L 9 HOH B 11 18 18 HOH HOH . L 9 HOH B 12 28 28 HOH HOH . L 9 HOH B 13 36 36 HOH HOH . L 9 HOH B 14 41 41 HOH HOH . L 9 HOH B 15 57 57 HOH HOH . M 9 HOH C 1 398 3 HOH HOH . M 9 HOH C 2 399 6 HOH HOH . M 9 HOH C 3 400 8 HOH HOH . M 9 HOH C 4 401 14 HOH HOH . M 9 HOH C 5 402 17 HOH HOH . M 9 HOH C 6 403 20 HOH HOH . M 9 HOH C 7 404 22 HOH HOH . M 9 HOH C 8 405 24 HOH HOH . M 9 HOH C 9 406 25 HOH HOH . M 9 HOH C 10 407 26 HOH HOH . M 9 HOH C 11 408 29 HOH HOH . M 9 HOH C 12 409 30 HOH HOH . M 9 HOH C 13 410 38 HOH HOH . M 9 HOH C 14 411 39 HOH HOH . M 9 HOH C 15 412 40 HOH HOH . M 9 HOH C 16 413 43 HOH HOH . M 9 HOH C 17 414 44 HOH HOH . M 9 HOH C 18 415 47 HOH HOH . M 9 HOH C 19 416 48 HOH HOH . M 9 HOH C 20 417 50 HOH HOH . M 9 HOH C 21 418 54 HOH HOH . M 9 HOH C 22 419 59 HOH HOH . M 9 HOH C 23 420 64 HOH HOH . M 9 HOH C 24 421 65 HOH HOH . M 9 HOH C 25 422 67 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 8 23.617 3.436 28.679 1 59.74 ? PG GSP 395 C 1 HETATM 2 O O3B GSP . . . J 8 22.674 3.411 27.319 1 49.1 ? O3B GSP 395 C 1 HETATM 3 S S1G GSP . . . J 8 25.175 4.355 28.097 1 56.67 ? S1G GSP 395 C 1 HETATM 4 O O2G GSP . . . J 8 22.788 3.983 29.486 1 60.88 ? O2G GSP 395 C 1 HETATM 5 O O3G GSP . . . J 8 24.197 2.079 28.975 1 61.56 ? O3G GSP 395 C 1 HETATM 6 P PB GSP . . . J 8 21.158 2.725 27.23 1 34.39 ? PB GSP 395 C 1 HETATM 7 O O1B GSP . . . J 8 21.47 1.548 26.475 1 37.35 ? O1B GSP 395 C 1 HETATM 8 O O2B GSP . . . J 8 20.415 2.431 28.475 1 38.28 ? O2B GSP 395 C 1 HETATM 9 P PA GSP . . . J 8 18.99 4.503 26.975 1 30.36 ? PA GSP 395 C 1 HETATM 10 O O1A GSP . . . J 8 17.909 3.497 27.291 1 34.59 ? O1A GSP 395 C 1 HETATM 11 O O2A GSP . . . J 8 19.5 5.518 27.977 1 28.07 ? O2A GSP 395 C 1 HETATM 12 O O3A GSP . . . J 8 20.237 3.751 26.386 1 34.57 ? O3A GSP 395 C 1 HETATM 13 O O5' GSP . . . J 8 18.454 5.37 25.695 1 27.26 ? O5' GSP 395 C 1 HETATM 14 C C5' GSP . . . J 8 19.226 6.449 25.11 1 27.63 ? C5' GSP 395 C 1 HETATM 15 C C4' GSP . . . J 8 18.244 7.478 24.6 1 25.44 ? C4' GSP 395 C 1 HETATM 16 O O4' GSP . . . J 8 17.508 6.92 23.455 1 26.39 ? O4' GSP 395 C 1 HETATM 17 C C3' GSP . . . J 8 17.114 7.807 25.613 1 26 ? C3' GSP 395 C 1 HETATM 18 O O3' GSP . . . J 8 17.006 9.252 25.605 1 29.93 ? O3' GSP 395 C 1 HETATM 19 C C2' GSP . . . J 8 15.799 7.171 25.059 1 24.05 ? C2' GSP 395 C 1 HETATM 20 O O2' GSP . . . J 8 14.634 7.949 25.355 1 31.89 ? O2' GSP 395 C 1 HETATM 21 C C1' GSP . . . J 8 16.068 7.103 23.543 1 24.24 ? C1' GSP 395 C 1 HETATM 22 N N9 GSP . . . J 8 15.478 5.921 22.842 1 20.33 ? N9 GSP 395 C 1 HETATM 23 C C8 GSP . . . J 8 15.454 4.603 23.148 1 15.76 ? C8 GSP 395 C 1 HETATM 24 N N7 GSP . . . J 8 14.854 3.856 22.306 1 16.83 ? N7 GSP 395 C 1 HETATM 25 C C5 GSP . . . J 8 14.438 4.732 21.323 1 16.8 ? C5 GSP 395 C 1 HETATM 26 C C6 GSP . . . J 8 13.699 4.452 20.097 1 17.03 ? C6 GSP 395 C 1 HETATM 27 O O6 GSP . . . J 8 13.348 3.31 19.783 1 11.54 ? O6 GSP 395 C 1 HETATM 28 N N1 GSP . . . J 8 13.479 5.649 19.388 1 20.31 ? N1 GSP 395 C 1 HETATM 29 C C2 GSP . . . J 8 13.894 6.944 19.767 1 24.6 ? C2 GSP 395 C 1 HETATM 30 N N2 GSP . . . J 8 13.626 7.992 19.006 1 26.98 ? N2 GSP 395 C 1 HETATM 31 N N3 GSP . . . J 8 14.582 7.171 20.923 1 24.65 ? N3 GSP 395 C 1 HETATM 32 C C4 GSP . . . J 8 14.813 6.014 21.646 1 20.65 ? C4 GSP 395 C 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #