data_7Z6R # _model_server_result.job_id uyPIhummtWVZjqXGmVmwZg _model_server_result.datetime_utc '2025-07-01 17:40:17' _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 7z6r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 7Z6R # _exptl.entry_id 7Z6R _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.48 _cell.angle_gamma 90 _cell.entry_id 7Z6R _cell.length_a 102.155 _cell.length_b 145.525 _cell.length_c 93.812 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Z6R _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G N N # _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 326 n n C1 O1 PRP sing 327 n n C1 O4 PRP sing 328 n n C1 H1 PRP sing 329 n n C2 C3 PRP sing 330 n n C2 O2 PRP sing 331 n n C2 H2 PRP sing 332 n n C3 C4 PRP sing 333 n n C3 O3 PRP sing 334 n n C3 H3 PRP sing 335 n n C4 C5 PRP sing 336 n n C4 O4 PRP sing 337 n n C4 H4 PRP sing 338 n n C5 O5 PRP sing 339 n n C5 H51 PRP sing 340 n n C5 H52 PRP sing 341 n n O1 PA PRP sing 342 n n O2 HO2 PRP sing 343 n n O3 HO3 PRP sing 344 n n O5 P PRP sing 345 n n P O1P PRP doub 346 n n P O2P PRP sing 347 n n P O3P PRP sing 348 n n O2P HOP2 PRP sing 349 n n O3P HOP3 PRP sing 350 n n PA O1A PRP doub 351 n n PA O2A PRP sing 352 n n PA O3A PRP sing 353 n n O2A HOA2 PRP sing 354 n n O3A PB PRP sing 355 n n PB O1B PRP doub 356 n n PB O2B PRP sing 357 n n PB O3B PRP sing 358 n n O2B HOB2 PRP sing 359 n n O3B HOB3 PRP sing 360 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 7Z6R _atom_sites.fract_transf_matrix[1][1] 0.009789 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002167 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006872 _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] 0.010918 _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 E 3 ATP C 1 401 401 ATP ATP . F 4 PRP C 1 402 501 PRP PRP . G 4 PRP D 1 501 501 PRP PRP . H 3 ATP D 1 502 401 ATP ATP . I 5 HOH A 1 401 13 HOH HOH . I 5 HOH A 2 402 16 HOH HOH . I 5 HOH A 3 403 7 HOH HOH . I 5 HOH A 4 404 5 HOH HOH . I 5 HOH A 5 405 9 HOH HOH . I 5 HOH A 6 406 8 HOH HOH . I 5 HOH A 7 407 12 HOH HOH . I 5 HOH A 8 408 6 HOH HOH . J 5 HOH B 1 401 3 HOH HOH . J 5 HOH B 2 402 14 HOH HOH . J 5 HOH B 3 403 1 HOH HOH . J 5 HOH B 4 404 10 HOH HOH . K 5 HOH C 1 501 2 HOH HOH . K 5 HOH C 2 502 15 HOH HOH . K 5 HOH C 3 503 11 HOH HOH . L 5 HOH D 1 601 4 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 . . . G 4 38.332 9.282 23.682 1 115.8 ? C1 PRP 501 D 1 HETATM 2 C C2 PRP . . . G 4 37.586 9.412 22.362 1 112.29 ? C2 PRP 501 D 1 HETATM 3 C C3 PRP . . . G 4 38.542 10.151 21.448 1 111.4 ? C3 PRP 501 D 1 HETATM 4 C C4 PRP . . . G 4 39.924 9.982 22.072 1 111.04 ? C4 PRP 501 D 1 HETATM 5 C C5 PRP . . . G 4 40.773 11.252 22.18 1 107.04 ? C5 PRP 501 D 1 HETATM 6 O O1 PRP . . . G 4 38.085 8.015 24.291 1 121.67 ? O1 PRP 501 D 1 HETATM 7 O O2 PRP . . . G 4 37.249 8.128 21.822 1 107.9 ? O2 PRP 501 D 1 HETATM 8 O O3 PRP . . . G 4 38.509 9.58 20.138 1 113.05 ? O3 PRP 501 D 1 HETATM 9 O O4 PRP . . . G 4 39.723 9.448 23.387 1 114.6 ? O4 PRP 501 D 1 HETATM 10 O O5 PRP . . . G 4 40.621 12.132 21.059 1 101.64 ? O5 PRP 501 D 1 HETATM 11 P P PRP . . . G 4 41.836 13.009 20.439 1 97.81 ? P PRP 501 D 1 HETATM 12 O O1P PRP . . . G 4 41.862 12.579 18.991 1 99.76 ? O1P PRP 501 D 1 HETATM 13 O O2P PRP . . . G 4 41.42 14.44 20.61 1 93.48 ? O2P PRP 501 D 1 HETATM 14 O O3P PRP . . . G 4 43.083 12.672 21.224 1 95.7 ? O3P PRP 501 D 1 HETATM 15 P PA PRP . . . G 4 38.777 7.615 25.692 1 126.81 ? PA PRP 501 D 1 HETATM 16 O O1A PRP . . . G 4 39.867 8.618 25.997 1 124.15 ? O1A PRP 501 D 1 HETATM 17 O O2A PRP . . . G 4 37.682 7.349 26.7 1 125.64 ? O2A PRP 501 D 1 HETATM 18 O O3A PRP . . . G 4 39.49 6.209 25.346 1 133.77 ? O3A PRP 501 D 1 HETATM 19 P PB PRP . . . G 4 39.003 4.8 25.971 1 139.37 ? PB PRP 501 D 1 HETATM 20 O O1B PRP . . . G 4 40.011 3.817 25.425 1 139.78 ? O1B PRP 501 D 1 HETATM 21 O O2B PRP . . . G 4 37.599 4.6 25.442 1 138.91 ? O2B PRP 501 D 1 HETATM 22 O O3B PRP . . . G 4 39.084 5.001 27.467 1 140.48 ? O3B PRP 501 D 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #