data_8WL9 # _model_server_result.job_id vHFmP9_JXcKYJXOvEB6YlA _model_server_result.datetime_utc '2024-11-23 01:28:02' _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 8wl9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8WL9 # _exptl.entry_id 8WL9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-ribopyranose _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 8WL9 _cell.length_a 66.85 _cell.length_b 110.68 _cell.length_c 37.26 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WL9 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C5 H10 O5' _chem_comp.formula_weight 150.13 _chem_comp.id RIP _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-ribopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms 'beta-D-ribose;D-ribose;ribose;RIBOSE(PYRANOSE FORM)' # 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 RIP sing 277 n n C1 O1 RIP sing 278 n n C1 O5 RIP sing 279 n n C1 H1 RIP sing 280 n n C2 C3 RIP sing 281 n n C2 O2 RIP sing 282 n n C2 H2 RIP sing 283 n n C3 C4 RIP sing 284 n n C3 O3 RIP sing 285 n n C3 H3 RIP sing 286 n n C4 C5 RIP sing 287 n n C4 O4 RIP sing 288 n n C4 H4 RIP sing 289 n n C5 O5 RIP sing 290 n n C5 H51 RIP sing 291 n n C5 H52 RIP sing 292 n n O1 HO1 RIP sing 293 n n O2 HO2 RIP sing 294 n n O3 HO3 RIP sing 295 n n O4 HO4 RIP sing 296 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version RIP DRibpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 RIP b-D-ribopyranose 'COMMON NAME' GMML 1 RIP b-D-Ribp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 RIP Rib 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 8WL9 _atom_sites.fract_transf_matrix[1][1] 0.014959 _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] 0.009035 _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] 0.026838 _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 RIP A 1 401 324 RIP RIP . C 3 HOH A 1 501 41 HOH HOH . C 3 HOH A 2 502 16 HOH HOH . C 3 HOH A 3 503 39 HOH HOH . C 3 HOH A 4 504 22 HOH HOH . C 3 HOH A 5 505 55 HOH HOH . C 3 HOH A 6 506 4 HOH HOH . C 3 HOH A 7 507 38 HOH HOH . C 3 HOH A 8 508 24 HOH HOH . C 3 HOH A 9 509 27 HOH HOH . C 3 HOH A 10 510 47 HOH HOH . C 3 HOH A 11 511 35 HOH HOH . C 3 HOH A 12 512 26 HOH HOH . C 3 HOH A 13 513 14 HOH HOH . C 3 HOH A 14 514 59 HOH HOH . C 3 HOH A 15 515 10 HOH HOH . C 3 HOH A 16 516 20 HOH HOH . C 3 HOH A 17 517 19 HOH HOH . C 3 HOH A 18 518 37 HOH HOH . C 3 HOH A 19 519 21 HOH HOH . C 3 HOH A 20 520 6 HOH HOH . C 3 HOH A 21 521 8 HOH HOH . C 3 HOH A 22 522 25 HOH HOH . C 3 HOH A 23 523 42 HOH HOH . C 3 HOH A 24 524 32 HOH HOH . C 3 HOH A 25 525 49 HOH HOH . C 3 HOH A 26 526 12 HOH HOH . C 3 HOH A 27 527 30 HOH HOH . C 3 HOH A 28 528 43 HOH HOH . C 3 HOH A 29 529 46 HOH HOH . C 3 HOH A 30 530 23 HOH HOH . C 3 HOH A 31 531 36 HOH HOH . C 3 HOH A 32 532 31 HOH HOH . C 3 HOH A 33 533 17 HOH HOH . C 3 HOH A 34 534 2 HOH HOH . C 3 HOH A 35 535 51 HOH HOH . C 3 HOH A 36 536 9 HOH HOH . C 3 HOH A 37 537 29 HOH HOH . C 3 HOH A 38 538 53 HOH HOH . C 3 HOH A 39 539 13 HOH HOH . C 3 HOH A 40 540 1 HOH HOH . C 3 HOH A 41 541 54 HOH HOH . C 3 HOH A 42 542 28 HOH HOH . C 3 HOH A 43 543 15 HOH HOH . C 3 HOH A 44 544 40 HOH HOH . C 3 HOH A 45 545 48 HOH HOH . C 3 HOH A 46 546 11 HOH HOH . C 3 HOH A 47 547 5 HOH HOH . C 3 HOH A 48 548 7 HOH HOH . C 3 HOH A 49 549 52 HOH HOH . C 3 HOH A 50 550 33 HOH HOH . C 3 HOH A 51 551 34 HOH HOH . C 3 HOH A 52 552 50 HOH HOH . C 3 HOH A 53 553 18 HOH HOH . C 3 HOH A 54 554 3 HOH HOH . C 3 HOH A 55 555 44 HOH HOH . C 3 HOH A 56 556 58 HOH HOH . C 3 HOH A 57 557 57 HOH HOH . C 3 HOH A 58 558 45 HOH HOH . C 3 HOH A 59 559 56 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 RIP . . . B 2 1.537 16.355 11.442 1 20.28 ? C1 RIP 401 A 1 HETATM 2 C C2 RIP . . . B 2 0.981 14.933 11.242 1 19.23 ? C2 RIP 401 A 1 HETATM 3 C C3 RIP . . . B 2 1.445 14.413 9.904 1 19.53 ? C3 RIP 401 A 1 HETATM 4 C C4 RIP . . . B 2 1.123 15.425 8.797 1 19.57 ? C4 RIP 401 A 1 HETATM 5 C C5 RIP . . . B 2 1.655 16.824 9.132 1 19.33 ? C5 RIP 401 A 1 HETATM 6 O O1 RIP . . . B 2 1.072 16.852 12.7 1 21.92 ? O1 RIP 401 A 1 HETATM 7 O O2 RIP . . . B 2 1.438 14.043 12.282 1 20.39 ? O2 RIP 401 A 1 HETATM 8 O O3 RIP . . . B 2 2.872 14.21 9.992 1 19.53 ? O3 RIP 401 A 1 HETATM 9 O O4 RIP . . . B 2 1.722 14.986 7.574 1 17.21 ? O4 RIP 401 A 1 HETATM 10 O O5 RIP . . . B 2 1.115 17.243 10.385 1 19.29 ? O5 RIP 401 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 703 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 10 #