data_1VST # _model_server_result.job_id U8yeWwSli7Bs7brr-WPMrg _model_server_result.datetime_utc '2025-09-07 09:50:56' _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 1vst # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 1VST # _exptl.entry_id 1VST _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.07 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose _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 120 _cell.entry_id 1VST _cell.length_a 122.2 _cell.length_b 122.2 _cell.length_c 62.2 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VST _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 61.1 105.828304 0 3 'crystal symmetry operation' 7_556 y,x,-z+4/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 82.933333 4 'crystal symmetry operation' 10_666 -y+1,-x+1,-z+4/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 61.1 105.828304 82.933333 # _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 B O1B GTP . A GTP 301 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc2 B O1A GTP . A GTP 301 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? # _chem_comp.formula 'C5 H13 O14 P3' _chem_comp.formula_weight 390.07 _chem_comp.id PRP _chem_comp.mon_nstd_flag n _chem_comp.name 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID;1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose;1-O-pyrophosphono-5-O-phosphono-D-ribose;1-O-pyrophosphono-5-O-phosphono-ribose' # 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 C1 C2 PRP sing 314 n n C1 O1 PRP sing 315 n n C1 O4 PRP sing 316 n n C1 H1 PRP sing 317 n n C2 C3 PRP sing 318 n n C2 O2 PRP sing 319 n n C2 H2 PRP sing 320 n n C3 C4 PRP sing 321 n n C3 O3 PRP sing 322 n n C3 H3 PRP sing 323 n n C4 C5 PRP sing 324 n n C4 O4 PRP sing 325 n n C4 H4 PRP sing 326 n n C5 O5 PRP sing 327 n n C5 H51 PRP sing 328 n n C5 H52 PRP sing 329 n n O1 PA PRP sing 330 n n O2 HO2 PRP sing 331 n n O3 HO3 PRP sing 332 n n O5 P PRP sing 333 n n P O1P PRP doub 334 n n P O2P PRP sing 335 n n P O3P PRP sing 336 n n O2P HOP2 PRP sing 337 n n O3P HOP3 PRP sing 338 n n PA O1A PRP doub 339 n n PA O2A PRP sing 340 n n PA O3A PRP sing 341 n n O2A HOA2 PRP sing 342 n n O3A PB PRP sing 343 n n PB O1B PRP doub 344 n n PB O2B PRP sing 345 n n PB O3B PRP sing 346 n n O2B HOB2 PRP sing 347 n n O3B HOB3 PRP sing 348 n n # _pdbx_chem_comp_identifier.comp_id PRP _pdbx_chem_comp_identifier.identifier a-D-Ribf1PO35PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 1VST _atom_sites.fract_transf_matrix[1][1] 0.008183 _atom_sites.fract_transf_matrix[1][2] 0.004725 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009449 _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] 0.016077 _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 B 2 GTP A 1 301 301 GTP GTP . C 3 MG A 1 302 302 MG MG2 . D 4 PRP A 1 303 303 PRP PRP . E 5 HOH A 1 401 401 HOH HOH . E 5 HOH A 2 402 402 HOH HOH . E 5 HOH A 3 403 403 HOH HOH . E 5 HOH A 4 404 404 HOH HOH . E 5 HOH A 5 406 406 HOH HOH . E 5 HOH A 6 407 407 HOH HOH . E 5 HOH A 7 408 408 HOH HOH . E 5 HOH A 8 409 409 HOH HOH . E 5 HOH A 9 410 410 HOH HOH . E 5 HOH A 10 411 411 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 C C1 PRP . . . D 4 35.446 78.264 31.715 1 20.1 ? C1 PRP 303 A 1 HETATM 2 C C2 PRP . . . D 4 35.201 76.8 31.318 1 20.09 ? C2 PRP 303 A 1 HETATM 3 C C3 PRP . . . D 4 36.475 76.45 30.561 1 19.71 ? C3 PRP 303 A 1 HETATM 4 C C4 PRP . . . D 4 36.825 77.738 29.851 1 19.72 ? C4 PRP 303 A 1 HETATM 5 C C5 PRP . . . D 4 36.442 77.741 28.411 1 17.71 ? C5 PRP 303 A 1 HETATM 6 O O1 PRP . . . D 4 36.269 78.294 32.924 1 23.12 ? O1 PRP 303 A 1 HETATM 7 O O2 PRP . . . D 4 34.958 76.018 32.499 1 19.58 ? O2 PRP 303 A 1 HETATM 8 O O3 PRP . . . D 4 37.484 76.081 31.54 1 22.58 ? O3 PRP 303 A 1 HETATM 9 O O4 PRP . . . D 4 36.128 78.813 30.63 1 19.39 ? O4 PRP 303 A 1 HETATM 10 O O5 PRP . . . D 4 36.394 79.044 27.825 1 16.68 ? O5 PRP 303 A 1 HETATM 11 P P PRP . . . D 4 37.374 79.563 26.67 1 16.17 ? P PRP 303 A 1 HETATM 12 O O1P PRP . . . D 4 38.71 79.937 27.263 1 16.13 ? O1P PRP 303 A 1 HETATM 13 O O2P PRP . . . D 4 37.463 78.47 25.618 1 17.03 ? O2P PRP 303 A 1 HETATM 14 O O3P PRP . . . D 4 36.641 80.786 26.164 1 18.59 ? O3P PRP 303 A 1 HETATM 15 P PA PRP . . . D 4 36.137 79.547 33.939 1 26.37 ? PA PRP 303 A 1 HETATM 16 O O1A PRP . . . D 4 37.336 80.423 33.818 1 28.7 ? O1A PRP 303 A 1 HETATM 17 O O2A PRP . . . D 4 34.836 80.254 33.695 1 27.11 ? O2A PRP 303 A 1 HETATM 18 O O3A PRP . . . D 4 36.173 78.757 35.339 1 26.32 ? O3A PRP 303 A 1 HETATM 19 P PB PRP . . . D 4 35.286 77.428 35.779 1 25.01 ? PB PRP 303 A 1 HETATM 20 O O1B PRP . . . D 4 36.222 76.273 35.434 1 26.01 ? O1B PRP 303 A 1 HETATM 21 O O2B PRP . . . D 4 34.012 77.442 34.956 1 26.76 ? O2B PRP 303 A 1 HETATM 22 O O3B PRP . . . D 4 35.03 77.58 37.248 1 26.32 ? O3B PRP 303 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #