data_2OBC # _model_server_result.job_id sUmSRWxMewC5SyEJe1Stwg _model_server_result.datetime_utc '2025-10-01 15:31:53' _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 2obc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 2OBC # _exptl.entry_id 2OBC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 230.11 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-O-phosphono-beta-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 2OBC _cell.length_a 173.1 _cell.length_b 173.1 _cell.length_c 76.7 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2OBC _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _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 C _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 covale ? covale1 A C TYR 33 A TYR 6 1_555 A N MSE 34 A MSE 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C MSE 34 A MSE 7 1_555 A N ALA 35 A ALA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale3 A C ARG 84 A ARG 57 1_555 A N MSE 85 A MSE 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C MSE 85 A MSE 58 1_555 A N ALA 86 A ALA 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C SER 126 A SER 99 1_555 A N MSE 127 A MSE 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale6 A C MSE 127 A MSE 100 1_555 A N GLN 128 A GLN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C LEU 153 A LEU 126 1_555 A N MSE 154 A MSE 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C MSE 154 A MSE 127 1_555 A N MSE 155 A MSE 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale9 A C MSE 155 A MSE 128 1_555 A N SER 156 A SER 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale10 A C ARG 168 A ARG 141 1_555 A N MSE 169 A MSE 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale11 A C MSE 169 A MSE 142 1_555 A N ARG 170 A ARG 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale12 A C ALA 189 A ALA 162 1_555 A N MSE 190 A MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale13 A C LEU 311 A LEU 284 1_555 A N MSE 312 A MSE 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale14 A C MSE 312 A MSE 285 1_555 A N MSE 313 A MSE 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale15 A C MSE 313 A MSE 286 1_555 A N GLN 314 A GLN 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 B C TYR 33 B TYR 6 1_555 B N MSE 34 B MSE 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale17 B C MSE 34 B MSE 7 1_555 B N ALA 35 B ALA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale18 B C ARG 84 B ARG 57 1_555 B N MSE 85 B MSE 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale19 B C MSE 85 B MSE 58 1_555 B N ALA 86 B ALA 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale20 B C SER 126 B SER 99 1_555 B N MSE 127 B MSE 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale21 B C MSE 127 B MSE 100 1_555 B N GLN 128 B GLN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale22 B C LEU 153 B LEU 126 1_555 B N MSE 154 B MSE 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale23 B C MSE 154 B MSE 127 1_555 B N MSE 155 B MSE 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale24 B C MSE 155 B MSE 128 1_555 B N SER 156 B SER 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale25 B C ARG 168 B ARG 141 1_555 B N MSE 169 B MSE 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale26 B C MSE 169 B MSE 142 1_555 B N ARG 170 B ARG 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale27 B C ALA 189 B ALA 162 1_555 B N MSE 190 B MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale28 B C MSE 190 B MSE 163 1_555 B N ALA 191 B ALA 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale29 B C LEU 311 B LEU 284 1_555 B N MSE 312 B MSE 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale30 B C MSE 312 B MSE 285 1_555 B N MSE 313 B MSE 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale31 B C MSE 313 B MSE 286 1_555 B N GLN 314 B GLN 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? # _chem_comp.formula 'C5 H11 O8 P' _chem_comp.formula_weight 230.11 _chem_comp.id RP5 _chem_comp.mon_nstd_flag n _chem_comp.name 5-O-phosphono-beta-D-ribofuranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms '[(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE;5-O-phosphono-beta-D-ribose;5-O-phosphono-D-ribose;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 O4 RP5 sing 296 n n C1 C2 RP5 sing 297 n n C1 O1 RP5 sing 298 n n C1 H1 RP5 sing 299 n n O4 C4 RP5 sing 300 n n C2 O2 RP5 sing 301 n n C2 C3 RP5 sing 302 n n C2 H2 RP5 sing 303 n n O2 HO2 RP5 sing 304 n n C3 O3 RP5 sing 305 n n C3 C4 RP5 sing 306 n n C3 H3 RP5 sing 307 n n O3 HO3 RP5 sing 308 n n C4 C5 RP5 sing 309 n n C4 H4 RP5 sing 310 n n C5 O5 RP5 sing 311 n n C5 H51 RP5 sing 312 n n C5 H52 RP5 sing 313 n n O5 P' RP5 sing 314 n n P' O1X RP5 doub 315 n n P' O2X RP5 sing 316 n n P' O3X RP5 sing 317 n n O2X HO' RP5 sing 318 n n O3X HOA RP5 sing 319 n n O1 HO1 RP5 sing 320 n n # _pdbx_chem_comp_identifier.comp_id RP5 _pdbx_chem_comp_identifier.identifier b-D-Ribf5PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1.0 # _atom_sites.entry_id 2OBC _atom_sites.fract_transf_matrix[1][1] 0.005777 _atom_sites.fract_transf_matrix[1][2] 0.003335 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006671 _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] 0.013038 _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 C 2 RP5 A 1 401 401 RP5 RP5 ? D 3 HOH A 1 402 5 HOH HOH ? D 3 HOH A 2 403 6 HOH HOH ? D 3 HOH A 3 404 7 HOH HOH ? D 3 HOH A 4 405 8 HOH HOH ? D 3 HOH A 5 406 10 HOH HOH ? D 3 HOH A 6 407 13 HOH HOH ? D 3 HOH A 7 408 14 HOH HOH ? D 3 HOH A 8 409 15 HOH HOH ? D 3 HOH A 9 410 17 HOH HOH ? D 3 HOH A 10 411 23 HOH HOH ? D 3 HOH A 11 412 24 HOH HOH ? D 3 HOH A 12 413 26 HOH HOH ? D 3 HOH A 13 414 31 HOH HOH ? D 3 HOH A 14 415 32 HOH HOH ? D 3 HOH A 15 416 35 HOH HOH ? D 3 HOH A 16 417 39 HOH HOH ? D 3 HOH A 17 418 42 HOH HOH ? D 3 HOH A 18 419 48 HOH HOH ? D 3 HOH A 19 420 51 HOH HOH ? D 3 HOH A 20 421 54 HOH HOH ? D 3 HOH A 21 422 61 HOH HOH ? D 3 HOH A 22 423 64 HOH HOH ? D 3 HOH A 23 424 71 HOH HOH ? D 3 HOH A 24 425 75 HOH HOH ? D 3 HOH A 25 426 76 HOH HOH ? D 3 HOH A 26 427 79 HOH HOH ? D 3 HOH A 27 428 86 HOH HOH ? D 3 HOH A 28 429 88 HOH HOH ? D 3 HOH A 29 430 89 HOH HOH ? D 3 HOH A 30 431 91 HOH HOH ? D 3 HOH A 31 432 94 HOH HOH ? E 3 HOH B 1 376 1 HOH HOH ? E 3 HOH B 2 377 2 HOH HOH ? E 3 HOH B 3 378 3 HOH HOH ? E 3 HOH B 4 379 4 HOH HOH ? E 3 HOH B 5 380 20 HOH HOH ? E 3 HOH B 6 381 25 HOH HOH ? E 3 HOH B 7 382 27 HOH HOH ? E 3 HOH B 8 383 30 HOH HOH ? E 3 HOH B 9 384 34 HOH HOH ? E 3 HOH B 10 385 44 HOH HOH ? E 3 HOH B 11 386 53 HOH HOH ? E 3 HOH B 12 387 55 HOH HOH ? E 3 HOH B 13 388 57 HOH HOH ? E 3 HOH B 14 389 73 HOH HOH ? E 3 HOH B 15 390 78 HOH HOH ? E 3 HOH B 16 391 85 HOH HOH ? E 3 HOH B 17 392 95 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 RP5 . . . C 2 59.918 51.775 30.757 1 82.53 ? C1 RP5 401 A 1 HETATM 2 O O4 RP5 . . . C 2 58.647 52.197 31.26 1 82.61 ? O4 RP5 401 A 1 HETATM 3 C C2 RP5 . . . C 2 59.729 51.348 29.311 1 82.27 ? C2 RP5 401 A 1 HETATM 4 O O2 RP5 . . . C 2 60.28 52.331 28.425 1 81.98 ? O2 RP5 401 A 1 HETATM 5 C C3 RP5 . . . C 2 58.225 51.199 29.142 1 81.98 ? C3 RP5 401 A 1 HETATM 6 O O3 RP5 . . . C 2 57.764 51.894 27.979 1 82.13 ? O3 RP5 401 A 1 HETATM 7 C C4 RP5 . . . C 2 57.58 51.792 30.392 1 81.63 ? C4 RP5 401 A 1 HETATM 8 C C5 RP5 . . . C 2 56.627 50.837 31.124 1 80.01 ? C5 RP5 401 A 1 HETATM 9 O O5 RP5 . . . C 2 55.604 50.332 30.253 1 78.04 ? O5 RP5 401 A 1 HETATM 10 P P' RP5 . . . C 2 54.255 49.626 30.795 1 76 ? P' RP5 401 A 1 HETATM 11 O O1X RP5 . . . C 2 53.304 50.782 30.931 1 77.3 ? O1X RP5 401 A 1 HETATM 12 O O2X RP5 . . . C 2 53.864 48.685 29.692 1 75.49 ? O2X RP5 401 A 1 HETATM 13 O O3X RP5 . . . C 2 54.623 48.971 32.107 1 76.05 ? O3X RP5 401 A 1 HETATM 14 O O1 RP5 . . . C 2 60.331 50.628 31.501 1 82.62 ? O1 RP5 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 213 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #