data_7Z8U # _model_server_result.job_id nPqtEUWhG1DrkRMs151WXw _model_server_result.datetime_utc '2024-12-01 09:04:10' _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 7z8u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7Z8U # _exptl.entry_id 7Z8U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.07 _entity.id 2 _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 103.52 _cell.angle_gamma 90 _cell.entry_id 7Z8U _cell.length_a 70.09 _cell.length_b 33.9 _cell.length_c 89.265 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Z8U _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 # 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_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 70.09 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 O2A PRP . A PRP 301 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc2 B O2B PRP . A PRP 301 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? metalc ? metalc3 C O1B ATP . A ATP 302 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc4 C O1A ATP . A ATP 302 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? # _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 7Z8U _atom_sites.fract_transf_matrix[1][1] 0.014267 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00343 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.029499 _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] 0.011522 _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 PRP A 1 301 301 PRP PRP . C 3 ATP A 1 302 401 ATP ATP . D 4 MG A 1 303 1 MG MG . E 5 HOH A 1 401 52 HOH HOH . E 5 HOH A 2 402 28 HOH HOH . E 5 HOH A 3 403 20 HOH HOH . E 5 HOH A 4 404 15 HOH HOH . E 5 HOH A 5 405 10 HOH HOH . E 5 HOH A 6 406 17 HOH HOH . E 5 HOH A 7 407 9 HOH HOH . E 5 HOH A 8 408 51 HOH HOH . E 5 HOH A 9 409 1 HOH HOH . E 5 HOH A 10 410 40 HOH HOH . E 5 HOH A 11 411 12 HOH HOH . E 5 HOH A 12 412 29 HOH HOH . E 5 HOH A 13 413 22 HOH HOH . E 5 HOH A 14 414 2 HOH HOH . E 5 HOH A 15 415 7 HOH HOH . E 5 HOH A 16 416 4 HOH HOH . E 5 HOH A 17 417 43 HOH HOH . E 5 HOH A 18 418 13 HOH HOH . E 5 HOH A 19 419 27 HOH HOH . E 5 HOH A 20 420 6 HOH HOH . E 5 HOH A 21 421 18 HOH HOH . E 5 HOH A 22 422 46 HOH HOH . E 5 HOH A 23 423 34 HOH HOH . E 5 HOH A 24 424 37 HOH HOH . E 5 HOH A 25 425 48 HOH HOH . E 5 HOH A 26 426 14 HOH HOH . E 5 HOH A 27 427 24 HOH HOH . E 5 HOH A 28 428 21 HOH HOH . E 5 HOH A 29 429 47 HOH HOH . E 5 HOH A 30 430 58 HOH HOH . E 5 HOH A 31 431 56 HOH HOH . E 5 HOH A 32 432 55 HOH HOH . E 5 HOH A 33 433 30 HOH HOH . E 5 HOH A 34 434 57 HOH HOH . E 5 HOH A 35 435 39 HOH HOH . E 5 HOH A 36 436 25 HOH HOH . E 5 HOH A 37 437 45 HOH HOH . E 5 HOH A 38 438 35 HOH HOH . E 5 HOH A 39 439 32 HOH HOH . E 5 HOH A 40 440 11 HOH HOH . E 5 HOH A 41 441 23 HOH HOH . E 5 HOH A 42 442 26 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 . . . B 2 29.145 -10.024 -9.805 1 38.04 ? C1 PRP 301 A 1 HETATM 2 C C2 PRP . . . B 2 29.637 -11.428 -10.101 1 34.97 ? C2 PRP 301 A 1 HETATM 3 C C3 PRP . . . B 2 30.025 -11.36 -11.566 1 32.01 ? C3 PRP 301 A 1 HETATM 4 C C4 PRP . . . B 2 29.456 -10.043 -12.063 1 28.52 ? C4 PRP 301 A 1 HETATM 5 C C5 PRP . . . B 2 28.621 -10.257 -13.295 1 24.34 ? C5 PRP 301 A 1 HETATM 6 O O1 PRP . . . B 2 30.265 -9.272 -9.37 1 46.58 ? O1 PRP 301 A 1 HETATM 7 O O2 PRP . . . B 2 30.749 -11.79 -9.262 1 36.25 ? O2 PRP 301 A 1 HETATM 8 O O3 PRP . . . B 2 31.426 -11.342 -11.779 1 29.15 ? O3 PRP 301 A 1 HETATM 9 O O4 PRP . . . B 2 28.662 -9.461 -11.02 1 31.96 ? O4 PRP 301 A 1 HETATM 10 O O5 PRP . . . B 2 27.967 -9.016 -13.554 1 19.47 ? O5 PRP 301 A 1 HETATM 11 P P PRP . . . B 2 27.993 -8.424 -15.02 1 15.58 ? P PRP 301 A 1 HETATM 12 O O1P PRP . . . B 2 27.746 -9.672 -15.843 1 13.81 ? O1P PRP 301 A 1 HETATM 13 O O2P PRP . . . B 2 26.921 -7.402 -14.915 1 13.81 ? O2P PRP 301 A 1 HETATM 14 O O3P PRP . . . B 2 29.385 -7.888 -15.314 1 14.86 ? O3P PRP 301 A 1 HETATM 15 P PA PRP . . . B 2 30.212 -8.402 -8.021 1 59.69 ? PA PRP 301 A 1 HETATM 16 O O1A PRP . . . B 2 29.852 -6.977 -8.36 1 54.89 ? O1A PRP 301 A 1 HETATM 17 O O2A PRP . . . B 2 29.396 -9.141 -6.958 1 54.42 ? O2A PRP 301 A 1 HETATM 18 O O3A PRP . . . B 2 31.792 -8.508 -7.714 1 59.87 ? O3A PRP 301 A 1 HETATM 19 P PB PRP . . . B 2 32.349 -9.821 -6.952 1 68.18 ? PB PRP 301 A 1 HETATM 20 O O1B PRP . . . B 2 33.405 -10.455 -7.835 1 55.69 ? O1B PRP 301 A 1 HETATM 21 O O2B PRP . . . B 2 31.147 -10.726 -6.726 1 67.3 ? O2B PRP 301 A 1 HETATM 22 O O3B PRP . . . B 2 32.854 -9.17 -5.675 1 68.66 ? O3B PRP 301 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 22 #