data_5YFX # _model_server_result.job_id jz377lgr50j0GCAIapvQlw _model_server_result.datetime_utc '2024-11-17 16:29:37' _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 5yfx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5YFX # _exptl.entry_id 5YFX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 310.09 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,5-di-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 5YFX _cell.length_a 81.13 _cell.length_b 81.13 _cell.length_c 100.18 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YFX _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_765 -y+2,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 121.695 70.260641 0 3 'crystal symmetry operation' 3_675 -x+y+1,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 140.521282 0 4 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 5_675 x-y+1,-y+2,-z 1 0 0 0 -1 0 0 0 -1 0 140.521282 0 6 'crystal symmetry operation' 6_765 -x+2,-x+y+1,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 121.695 70.260641 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 H12 O11 P2' _chem_comp.formula_weight 310.09 _chem_comp.id RI2 _chem_comp.mon_nstd_flag n _chem_comp.name 1,5-di-O-phosphono-alpha-D-ribofuranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms 1,5-di-O-phosphono-alpha-D-ribose;1,5-di-O-phosphono-D-ribose;1,5-di-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 O1P P RI2 doub 316 n n O5 P RI2 sing 317 n n P O3P RI2 sing 318 n n P O2P RI2 sing 319 n n C2 C1 RI2 sing 320 n n O1 C1 RI2 sing 321 n n C1 O4 RI2 sing 322 n n C1 H1 RI2 sing 323 n n O1 PA RI2 sing 324 n n O2 C2 RI2 sing 325 n n C2 C3 RI2 sing 326 n n C2 H2 RI2 sing 327 n n O2 HO2 RI2 sing 328 n n O3 C3 RI2 sing 329 n n C3 C4 RI2 sing 330 n n C3 H3 RI2 sing 331 n n O3 HO3 RI2 sing 332 n n C4 O4 RI2 sing 333 n n C4 C5 RI2 sing 334 n n C4 H4 RI2 sing 335 n n C5 O5 RI2 sing 336 n n C5 H51 RI2 sing 337 n n C5 H52 RI2 sing 338 n n O2A PA RI2 doub 339 n n PA O1A RI2 sing 340 n n PA O3A RI2 sing 341 n n O1A HO1A RI2 sing 342 n n O2P HO2P RI2 sing 343 n n O3A HO3A RI2 sing 344 n n O3P HO3P RI2 sing 345 n n # _pdbx_chem_comp_identifier.comp_id RI2 _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 5YFX _atom_sites.fract_transf_matrix[1][1] 0.012326 _atom_sites.fract_transf_matrix[1][2] 0.007116 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014233 _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] 0.009982 _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 RI2 A 1 401 1 RI2 RI2 . C 3 AMP A 1 402 2 AMP AMP . D 4 HOH A 1 501 32 HOH HOH . D 4 HOH A 2 502 27 HOH HOH . D 4 HOH A 3 503 45 HOH HOH . D 4 HOH A 4 504 34 HOH HOH . D 4 HOH A 5 505 40 HOH HOH . D 4 HOH A 6 506 11 HOH HOH . D 4 HOH A 7 507 10 HOH HOH . D 4 HOH A 8 508 37 HOH HOH . D 4 HOH A 9 509 42 HOH HOH . D 4 HOH A 10 510 24 HOH HOH . D 4 HOH A 11 511 39 HOH HOH . D 4 HOH A 12 512 26 HOH HOH . D 4 HOH A 13 513 28 HOH HOH . D 4 HOH A 14 514 9 HOH HOH . D 4 HOH A 15 515 6 HOH HOH . D 4 HOH A 16 516 22 HOH HOH . D 4 HOH A 17 517 13 HOH HOH . D 4 HOH A 18 518 14 HOH HOH . D 4 HOH A 19 519 12 HOH HOH . D 4 HOH A 20 520 18 HOH HOH . D 4 HOH A 21 521 30 HOH HOH . D 4 HOH A 22 522 16 HOH HOH . D 4 HOH A 23 523 17 HOH HOH . D 4 HOH A 24 524 8 HOH HOH . D 4 HOH A 25 525 44 HOH HOH . D 4 HOH A 26 526 35 HOH HOH . D 4 HOH A 27 527 25 HOH HOH . D 4 HOH A 28 528 19 HOH HOH . D 4 HOH A 29 529 15 HOH HOH . D 4 HOH A 30 530 7 HOH HOH . D 4 HOH A 31 531 5 HOH HOH . D 4 HOH A 32 532 23 HOH HOH . D 4 HOH A 33 533 36 HOH HOH . D 4 HOH A 34 534 2 HOH HOH . D 4 HOH A 35 535 41 HOH HOH . D 4 HOH A 36 536 1 HOH HOH . D 4 HOH A 37 537 31 HOH HOH . D 4 HOH A 38 538 4 HOH HOH . D 4 HOH A 39 539 38 HOH HOH . D 4 HOH A 40 540 33 HOH HOH . D 4 HOH A 41 541 21 HOH HOH . D 4 HOH A 42 542 29 HOH HOH . D 4 HOH A 43 543 3 HOH HOH . D 4 HOH A 44 544 20 HOH HOH . D 4 HOH A 45 545 43 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 P RI2 . . . B 2 25.225 51.109 19.825 1 33.27 ? P RI2 401 A 1 HETATM 2 C C1 RI2 . . . B 2 27.66 48.172 16.184 1 33.44 ? C1 RI2 401 A 1 HETATM 3 O O1 RI2 . . . B 2 28.645 47.18 15.911 1 34.93 ? O1 RI2 401 A 1 HETATM 4 C C2 RI2 . . . B 2 27.685 49.234 15.101 1 34.37 ? C2 RI2 401 A 1 HETATM 5 O O2 RI2 . . . B 2 29.034 49.572 14.689 1 35.93 ? O2 RI2 401 A 1 HETATM 6 C C3 RI2 . . . B 2 27.097 50.43 15.809 1 32.91 ? C3 RI2 401 A 1 HETATM 7 O O3 RI2 . . . B 2 27.368 51.666 15.131 1 31.28 ? O3 RI2 401 A 1 HETATM 8 C C4 RI2 . . . B 2 27.823 50.288 17.139 1 31.47 ? C4 RI2 401 A 1 HETATM 9 O O4 RI2 . . . B 2 27.922 48.883 17.411 1 31.83 ? O4 RI2 401 A 1 HETATM 10 C C5 RI2 . . . B 2 27.171 51.031 18.259 1 30.98 ? C5 RI2 401 A 1 HETATM 11 O O5 RI2 . . . B 2 25.876 50.55 18.493 1 30.14 ? O5 RI2 401 A 1 HETATM 12 P PA RI2 . . . B 2 28.351 45.592 15.978 1 39.47 ? PA RI2 401 A 1 HETATM 13 O O1A RI2 . . . B 2 28.741 45.136 17.39 1 35.52 ? O1A RI2 401 A 1 HETATM 14 O O1P RI2 . . . B 2 25.033 52.616 19.826 1 34.74 ? O1P RI2 401 A 1 HETATM 15 O O2A RI2 . . . B 2 29.196 44.859 14.961 1 36.52 ? O2A RI2 401 A 1 HETATM 16 O O2P RI2 . . . B 2 26.159 50.713 20.951 1 34.12 ? O2P RI2 401 A 1 HETATM 17 O O3A RI2 . . . B 2 26.937 45.383 15.524 1 33.06 ? O3A RI2 401 A 1 HETATM 18 O O3P RI2 . . . B 2 23.845 50.517 19.942 1 36.35 ? O3P RI2 401 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 410 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 18 #