data_1CUL # _model_server_result.job_id FiqjDeOoIhD71LOtoV3o7Q _model_server_result.datetime_utc '2024-10-26 20:32:06' _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 1cul # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":395}' # _entry.id 1CUL # _exptl.entry_id 1CUL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 10 _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 1CUL _cell.length_a 118.2 _cell.length_b 133.6 _cell.length_c 70.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CUL _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA hexameric 6 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,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 10 _struct_asym.id N _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 G O1A 3PO . A 3PO 1003 1_555 I O1P 103 . B 103 1082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? covale ? covale2 G PA 3PO . A 3PO 1003 1_555 I O2P 103 . B 103 1082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale3 G O2A 3PO . A 3PO 1003 1_555 I P 103 . B 103 1082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? metalc ? metalc1 A OD1 ASP 33 A ASP 396 1_555 D MG MG . A MG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc2 A OD2 ASP 33 A ASP 396 1_555 E MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? metalc ? metalc3 A O ILE 34 A ILE 397 1_555 D MG MG . A MG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc4 A OD1 ASP 77 A ASP 440 1_555 D MG MG . A MG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc5 A OD1 ASP 77 A ASP 440 1_555 E MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.035 ? metalc ? metalc6 A OD2 ASP 77 A ASP 440 1_555 E MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc7 G O2B 3PO . A 3PO 1003 1_555 D MG MG . A MG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc8 G O2G 3PO . A 3PO 1003 1_555 D MG MG . A MG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc9 G O5' 3PO . A 3PO 1003 1_555 E MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc10 G O1A 3PO . A 3PO 1003 1_555 E MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc11 E MG MG . A MG 1007 1_555 I O1P 103 . B 103 1082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc12 C OG SER 54 C SER 54 1_555 K MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc13 C OG1 THR 190 C THR 204 1_555 K MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc14 N O2B GSP . C GSP 395 1_555 K MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? metalc ? metalc15 N O2G GSP . C GSP 395 1_555 K MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc16 N O3B GSP . C GSP 395 1_555 K MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.063 ? metalc ? metalc17 K MG MG . C MG 396 1_555 Q O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc18 K MG MG . C MG 396 1_555 Q O HOH . C HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? # _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 248 n n PG S1G GSP doub 249 n n PG O2G GSP sing 250 n n PG O3G GSP sing 251 n n O3B PB GSP sing 252 n n O2G HOG2 GSP sing 253 n n O3G HOG3 GSP sing 254 n n PB O1B GSP doub 255 n n PB O2B GSP sing 256 n n PB O3A GSP sing 257 n n O2B HOB2 GSP sing 258 n n PA O1A GSP doub 259 n n PA O2A GSP sing 260 n n PA O3A GSP sing 261 n n PA O5' GSP sing 262 n n O2A HOA2 GSP sing 263 n n O5' C5' GSP sing 264 n n C5' C4' GSP sing 265 n n C5' "H5'1" GSP sing 266 n n C5' "H5'2" GSP sing 267 n n C4' O4' GSP sing 268 n n C4' C3' GSP sing 269 n n C4' H4' GSP sing 270 n n O4' C1' GSP sing 271 n n C3' O3' GSP sing 272 n n C3' C2' GSP sing 273 n n C3' H3' GSP sing 274 n n O3' HO3' GSP sing 275 n n C2' O2' GSP sing 276 n n C2' C1' GSP sing 277 n n C2' H2' GSP sing 278 n n O2' HO2' GSP sing 279 n n C1' N9 GSP sing 280 n n C1' H1' GSP sing 281 n n N9 C8 GSP sing 282 n y N9 C4 GSP sing 283 n y C8 N7 GSP doub 284 n y C8 H8 GSP sing 285 n n N7 C5 GSP sing 286 n y C5 C6 GSP sing 287 n n C5 C4 GSP doub 288 n y C6 O6 GSP doub 289 n n C6 N1 GSP sing 290 n n N1 C2 GSP sing 291 n n N1 HN1 GSP sing 292 n n C2 N2 GSP sing 293 n n C2 N3 GSP doub 294 n n N2 HN21 GSP sing 295 n n N2 HN22 GSP sing 296 n n N3 C4 GSP sing 297 n n # _atom_sites.entry_id 1CUL _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] 0.007485 _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] 0.014164 _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 MG A 1 1006 1006 MG MG . E 4 MG A 1 1007 1007 MG MG . F 5 FOK A 1 1001 1001 FOK FOK . G 6 3PO A 1 1003 1003 3PO 3PO . H 7 MES A 1 1004 1004 MES MES . I 8 103 B 1 1082 1002 103 103 . J 7 MES B 1 1083 1005 MES MES . K 4 MG C 1 396 396 MG MG . L 9 CL C 1 397 397 CL CL . M 9 CL C 1 398 398 CL CL . N 10 GSP C 1 395 395 GSP GSP . O 11 HOH A 1 11 11 HOH HOH . O 11 HOH A 2 19 19 HOH HOH . O 11 HOH A 3 20 20 HOH HOH . O 11 HOH A 4 23 23 HOH HOH . O 11 HOH A 5 24 24 HOH HOH . O 11 HOH A 6 30 30 HOH HOH . O 11 HOH A 7 31 31 HOH HOH . O 11 HOH A 8 32 32 HOH HOH . O 11 HOH A 9 33 33 HOH HOH . O 11 HOH A 10 57 57 HOH HOH . O 11 HOH A 11 59 59 HOH HOH . O 11 HOH A 12 76 76 HOH HOH . O 11 HOH A 13 81 81 HOH HOH . O 11 HOH A 14 82 82 HOH HOH . P 11 HOH B 1 8 8 HOH HOH . P 11 HOH B 2 12 12 HOH HOH . P 11 HOH B 3 13 13 HOH HOH . P 11 HOH B 4 14 14 HOH HOH . P 11 HOH B 5 15 15 HOH HOH . P 11 HOH B 6 16 16 HOH HOH . P 11 HOH B 7 17 17 HOH HOH . P 11 HOH B 8 18 18 HOH HOH . P 11 HOH B 9 21 21 HOH HOH . P 11 HOH B 10 22 22 HOH HOH . P 11 HOH B 11 25 25 HOH HOH . P 11 HOH B 12 26 26 HOH HOH . P 11 HOH B 13 27 27 HOH HOH . P 11 HOH B 14 28 28 HOH HOH . P 11 HOH B 15 34 34 HOH HOH . P 11 HOH B 16 36 36 HOH HOH . P 11 HOH B 17 37 37 HOH HOH . P 11 HOH B 18 38 38 HOH HOH . P 11 HOH B 19 54 54 HOH HOH . P 11 HOH B 20 55 55 HOH HOH . P 11 HOH B 21 56 56 HOH HOH . P 11 HOH B 22 58 58 HOH HOH . P 11 HOH B 23 60 60 HOH HOH . P 11 HOH B 24 61 61 HOH HOH . P 11 HOH B 25 62 62 HOH HOH . P 11 HOH B 26 73 73 HOH HOH . P 11 HOH B 27 77 77 HOH HOH . P 11 HOH B 28 78 78 HOH HOH . P 11 HOH B 29 80 80 HOH HOH . P 11 HOH B 30 83 83 HOH HOH . P 11 HOH B 31 84 84 HOH HOH . P 11 HOH B 32 85 85 HOH HOH . P 11 HOH B 33 86 86 HOH HOH . Q 11 HOH C 1 399 1 HOH HOH . Q 11 HOH C 2 400 2 HOH HOH . Q 11 HOH C 3 401 3 HOH HOH . Q 11 HOH C 4 402 4 HOH HOH . Q 11 HOH C 5 403 5 HOH HOH . Q 11 HOH C 6 404 7 HOH HOH . Q 11 HOH C 7 405 10 HOH HOH . Q 11 HOH C 8 406 29 HOH HOH . Q 11 HOH C 9 407 35 HOH HOH . Q 11 HOH C 10 408 39 HOH HOH . Q 11 HOH C 11 409 40 HOH HOH . Q 11 HOH C 12 410 41 HOH HOH . Q 11 HOH C 13 411 42 HOH HOH . Q 11 HOH C 14 412 43 HOH HOH . Q 11 HOH C 15 413 44 HOH HOH . Q 11 HOH C 16 414 45 HOH HOH . Q 11 HOH C 17 415 46 HOH HOH . Q 11 HOH C 18 416 47 HOH HOH . Q 11 HOH C 19 417 48 HOH HOH . Q 11 HOH C 20 418 49 HOH HOH . Q 11 HOH C 21 419 50 HOH HOH . Q 11 HOH C 22 420 51 HOH HOH . Q 11 HOH C 23 421 52 HOH HOH . Q 11 HOH C 24 422 53 HOH HOH . Q 11 HOH C 25 423 63 HOH HOH . Q 11 HOH C 26 424 65 HOH HOH . Q 11 HOH C 27 425 67 HOH HOH . Q 11 HOH C 28 426 68 HOH HOH . Q 11 HOH C 29 427 69 HOH HOH . Q 11 HOH C 30 428 71 HOH HOH . Q 11 HOH C 31 429 72 HOH HOH . Q 11 HOH C 32 430 74 HOH HOH . Q 11 HOH C 33 431 75 HOH HOH . Q 11 HOH C 34 432 79 HOH HOH . Q 11 HOH C 35 433 88 HOH HOH . Q 11 HOH C 36 434 89 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 . . . N 10 23.603 3.028 28.645 1 46.3 ? PG GSP 395 C 1 HETATM 2 O O3B GSP . . . N 10 22.41 3.216 27.736 1 43.06 ? O3B GSP 395 C 1 HETATM 3 S S1G GSP . . . N 10 24.915 4.436 28.581 1 53.55 ? S1G GSP 395 C 1 HETATM 4 O O2G GSP . . . N 10 23.126 3.086 30.052 1 48.31 ? O2G GSP 395 C 1 HETATM 5 O O3G GSP . . . N 10 24.342 1.828 28.188 1 45.79 ? O3G GSP 395 C 1 HETATM 6 P PB GSP . . . N 10 21.059 2.589 27.522 1 35.56 ? PB GSP 395 C 1 HETATM 7 O O1B GSP . . . N 10 21.224 1.42 26.62 1 31.64 ? O1B GSP 395 C 1 HETATM 8 O O2B GSP . . . N 10 20.437 2.385 28.85 1 36.03 ? O2B GSP 395 C 1 HETATM 9 P PA GSP . . . N 10 18.952 4.298 27.095 1 29.74 ? PA GSP 395 C 1 HETATM 10 O O1A GSP . . . N 10 17.957 3.229 27.377 1 31.6 ? O1A GSP 395 C 1 HETATM 11 O O2A GSP . . . N 10 19.189 5.357 28.095 1 26.04 ? O2A GSP 395 C 1 HETATM 12 O O3A GSP . . . N 10 20.272 3.645 26.782 1 34.14 ? O3A GSP 395 C 1 HETATM 13 O O5' GSP . . . N 10 18.502 5.004 25.741 1 27.9 ? O5' GSP 395 C 1 HETATM 14 C C5' GSP . . . N 10 19.205 6.138 25.248 1 30.13 ? C5' GSP 395 C 1 HETATM 15 C C4' GSP . . . N 10 18.24 7.165 24.705 1 33.01 ? C4' GSP 395 C 1 HETATM 16 O O4' GSP . . . N 10 17.597 6.686 23.503 1 33.39 ? O4' GSP 395 C 1 HETATM 17 C C3' GSP . . . N 10 17.112 7.585 25.645 1 31.38 ? C3' GSP 395 C 1 HETATM 18 O O3' GSP . . . N 10 16.894 8.982 25.489 1 30.88 ? O3' GSP 395 C 1 HETATM 19 C C2' GSP . . . N 10 15.916 6.825 25.11 1 31.37 ? C2' GSP 395 C 1 HETATM 20 O O2' GSP . . . N 10 14.688 7.483 25.354 1 32.56 ? O2' GSP 395 C 1 HETATM 21 C C1' GSP . . . N 10 16.191 6.794 23.624 1 28.66 ? C1' GSP 395 C 1 HETATM 22 N N9 GSP . . . N 10 15.597 5.653 22.944 1 29.13 ? N9 GSP 395 C 1 HETATM 23 C C8 GSP . . . N 10 15.686 4.333 23.311 1 22.9 ? C8 GSP 395 C 1 HETATM 24 N N7 GSP . . . N 10 15.043 3.533 22.504 1 27.41 ? N7 GSP 395 C 1 HETATM 25 C C5 GSP . . . N 10 14.499 4.378 21.541 1 28.8 ? C5 GSP 395 C 1 HETATM 26 C C6 GSP . . . N 10 13.706 4.078 20.408 1 27.42 ? C6 GSP 395 C 1 HETATM 27 O O6 GSP . . . N 10 13.327 2.981 20.006 1 34.02 ? O6 GSP 395 C 1 HETATM 28 N N1 GSP . . . N 10 13.361 5.224 19.711 1 23.4 ? N1 GSP 395 C 1 HETATM 29 C C2 GSP . . . N 10 13.733 6.503 20.052 1 29.5 ? C2 GSP 395 C 1 HETATM 30 N N2 GSP . . . N 10 13.284 7.5 19.254 1 23.05 ? N2 GSP 395 C 1 HETATM 31 N N3 GSP . . . N 10 14.488 6.788 21.102 1 28.78 ? N3 GSP 395 C 1 HETATM 32 C C4 GSP . . . N 10 14.83 5.688 21.798 1 29.12 ? C4 GSP 395 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #