data_9RUB # _model_server_result.job_id ydiTQIPfZMyXrfRTpm-BpQ _model_server_result.datetime_utc '2025-03-26 20:11:27' _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 9rub # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":600}' # _entry.id 9RUB # _exptl.entry_id 9RUB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 310.09 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description RIBULOSE-1,5-DIPHOSPHATE _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 92.1 _cell.angle_gamma 90 _cell.entry_id 9RUB _cell.length_a 65.5 _cell.length_b 70.6 _cell.length_c 104.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9RUB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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,F,G,H _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 ? 2 C N N ? 2 F N 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 NZ LYS 191 A LYS 191 1_555 E C FMT . A FMT 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 B NZ LYS 191 B LYS 191 1_555 H C FMT . B FMT 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? metalc ? metalc1 A OD1 ASP 193 A ASP 193 1_555 D MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc2 D MG MG . A MG 500 1_555 C O2 RUB . A RUB 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc3 D MG MG . A MG 500 1_555 C O3 RUB . A RUB 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc4 D MG MG . A MG 500 1_555 E O1 FMT . A FMT 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc5 D MG MG . A MG 500 1_555 E O2 FMT . A FMT 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc6 B OD1 ASP 193 B ASP 193 1_555 G MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc7 G MG MG . B MG 500 1_555 F O3 RUB . B RUB 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc8 G MG MG . B MG 500 1_555 F O2 RUB . B RUB 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc9 G MG MG . B MG 500 1_555 H O1 FMT . B FMT 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? # _chem_comp.formula 'C5 H12 O11 P2' _chem_comp.formula_weight 310.09 _chem_comp.id RUB _chem_comp.mon_nstd_flag . _chem_comp.name RIBULOSE-1,5-DIPHOSPHATE _chem_comp.type saccharide _chem_comp.pdbx_synonyms ? # 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 RUB sing 279 n n C1 O1 RUB sing 280 n n C1 H11 RUB sing 281 n n C1 H12 RUB sing 282 n n C2 C3 RUB sing 283 n n C2 O2 RUB doub 284 n n C3 C4 RUB sing 285 n n C3 O3 RUB sing 286 n n C3 H3 RUB sing 287 n n C4 C5 RUB sing 288 n n C4 O4 RUB sing 289 n n C4 H4 RUB sing 290 n n C5 O5 RUB sing 291 n n C5 H51 RUB sing 292 n n C5 H52 RUB sing 293 n n O1 P1 RUB sing 294 n n O3 HO3 RUB sing 295 n n O4 HO4 RUB sing 296 n n O5 P2 RUB sing 297 n n P1 O1P RUB doub 298 n n P1 O2P RUB sing 299 n n P1 O3P RUB sing 300 n n P2 O4P RUB doub 301 n n P2 O5P RUB sing 302 n n P2 O6P RUB sing 303 n n O2P HOP2 RUB sing 304 n n O3P HOP3 RUB sing 305 n n O5P HOP5 RUB sing 306 n n O6P HOP6 RUB sing 307 n n # _atom_sites.entry_id 9RUB _atom_sites.fract_transf_matrix[1][1] 0.015267 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00056 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014164 _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] 0.009613 _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 RUB A 1 600 600 RUB RUB . D 3 MG A 1 500 500 MG MG . E 4 FMT A 1 601 191 FMT CBX . F 2 RUB B 1 700 700 RUB RUB . G 3 MG B 1 500 500 MG MG . H 4 FMT B 1 701 191 FMT CBX . # 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 RUB . . . C 2 29.734 18.079 34.574 1 22.22 ? C1 RUB 600 A 1 HETATM 2 C C2 RUB . . . C 2 31.209 17.53 34.589 1 21.15 ? C2 RUB 600 A 1 HETATM 3 C C3 RUB . . . C 2 31.415 15.969 34.905 1 20.87 ? C3 RUB 600 A 1 HETATM 4 C C4 RUB . . . C 2 32.056 15.112 33.742 1 20.81 ? C4 RUB 600 A 1 HETATM 5 C C5 RUB . . . C 2 31.277 13.711 33.544 1 21.37 ? C5 RUB 600 A 1 HETATM 6 O O1 RUB . . . C 2 29.414 17.657 35.915 1 23.47 ? O1 RUB 600 A 1 HETATM 7 O O2 RUB . . . C 2 32.144 18.328 34.373 1 20.58 ? O2 RUB 600 A 1 HETATM 8 O O3 RUB . . . C 2 32.273 15.777 36.008 1 20.96 ? O3 RUB 600 A 1 HETATM 9 O O4 RUB . . . C 2 31.99 15.819 32.506 1 20.27 ? O4 RUB 600 A 1 HETATM 10 O O5 RUB . . . C 2 31.681 12.622 34.496 1 21.75 ? O5 RUB 600 A 1 HETATM 11 P P1 RUB . . . C 2 27.942 17.08 36.354 1 24.39 ? P1 RUB 600 A 1 HETATM 12 P P2 RUB . . . C 2 31.019 11.072 34.393 1 22.6 ? P2 RUB 600 A 1 HETATM 13 O O1P RUB . . . C 2 26.798 18.182 36.137 1 23.16 ? O1P RUB 600 A 1 HETATM 14 O O2P RUB . . . C 2 28.006 16.623 37.893 1 23.21 ? O2P RUB 600 A 1 HETATM 15 O O3P RUB . . . C 2 27.493 15.805 35.493 1 23.44 ? O3P RUB 600 A 1 HETATM 16 O O4P RUB . . . C 2 29.841 10.968 33.303 1 20.74 ? O4P RUB 600 A 1 HETATM 17 O O5P RUB . . . C 2 30.501 10.567 35.852 1 20.09 ? O5P RUB 600 A 1 HETATM 18 O O6P RUB . . . C 2 32.064 9.97 33.909 1 22.68 ? O6P RUB 600 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 18 #