data_7UF4 # _model_server_result.job_id ITqxiA1wB8TTf37KKC_ypg _model_server_result.datetime_utc '2024-10-17 19:32:00' _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 7uf4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7UF4 # _exptl.entry_id 7UF4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 212.095 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2-hydroxy-3,4-dioxopentyl dihydrogen phosphate' _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 7UF4 _cell.length_a 60.337 _cell.length_b 78.558 _cell.length_c 90.535 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7UF4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 21' # _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,I _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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 45.2675 # _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 A OE1 GLU 39 A GLU 39 1_555 D MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc2 A ND1 HIS 154 A HIS 154 1_555 D MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc3 B O05 N46 . A N46 301 1_555 D MN MN . A MN 303 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc4 C O13 5RP . A 5RP 302 1_555 D MN MN . A MN 303 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc5 C O14 5RP . A 5RP 302 1_555 D MN MN . A MN 303 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc6 D MN MN . A MN 303 1_555 I O HOH . A HOH 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? # _chem_comp.formula 'C5 H9 O7 P' _chem_comp.formula_weight 212.095 _chem_comp.id N46 _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-2-hydroxy-3,4-dioxopentyl dihydrogen phosphate' _chem_comp.type non-polymer _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 O10 P08 N46 doub 270 n n O09 P08 N46 sing 271 n n O11 P08 N46 sing 272 n n P08 O07 N46 sing 273 n n O07 C06 N46 sing 274 n n O05 C04 N46 sing 275 n n C06 C04 N46 sing 276 n n O12 C03 N46 doub 277 n n C04 C03 N46 sing 278 n n C03 C02 N46 sing 279 n n O13 C02 N46 doub 280 n n C02 C01 N46 sing 281 n n C01 H011 N46 sing 282 n n C01 H012 N46 sing 283 n n C01 H013 N46 sing 284 n n C04 H041 N46 sing 285 n n C06 H061 N46 sing 286 n n C06 H062 N46 sing 287 n n O05 H051 N46 sing 288 n n O09 H1 N46 sing 289 n n O11 H2 N46 sing 290 n n # _atom_sites.entry_id 7UF4 _atom_sites.fract_transf_matrix[1][1] 0.016574 _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] 0.012729 _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] 0.011045 _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 N46 A 1 301 1 N46 LIG . C 3 5RP A 1 302 1 5RP 5RP . D 4 MN A 1 303 1 MN MN . E 4 MN A 1 304 2 MN MN . F 5 EDO A 1 305 1 EDO EDO . G 5 EDO A 1 306 2 EDO EDO . H 5 EDO A 1 307 3 EDO EDO . I 6 HOH A 1 401 51 HOH HOH . I 6 HOH A 2 402 12 HOH HOH . I 6 HOH A 3 403 20 HOH HOH . I 6 HOH A 4 404 34 HOH HOH . I 6 HOH A 5 405 16 HOH HOH . I 6 HOH A 6 406 6 HOH HOH . I 6 HOH A 7 407 44 HOH HOH . I 6 HOH A 8 408 10 HOH HOH . I 6 HOH A 9 409 8 HOH HOH . I 6 HOH A 10 410 3 HOH HOH . I 6 HOH A 11 411 7 HOH HOH . I 6 HOH A 12 412 52 HOH HOH . I 6 HOH A 13 413 11 HOH HOH . I 6 HOH A 14 414 31 HOH HOH . I 6 HOH A 15 415 14 HOH HOH . I 6 HOH A 16 416 25 HOH HOH . I 6 HOH A 17 417 13 HOH HOH . I 6 HOH A 18 418 40 HOH HOH . I 6 HOH A 19 419 19 HOH HOH . I 6 HOH A 20 420 1 HOH HOH . I 6 HOH A 21 421 4 HOH HOH . I 6 HOH A 22 422 5 HOH HOH . I 6 HOH A 23 423 18 HOH HOH . I 6 HOH A 24 424 2 HOH HOH . I 6 HOH A 25 425 22 HOH HOH . I 6 HOH A 26 426 23 HOH HOH . I 6 HOH A 27 427 36 HOH HOH . I 6 HOH A 28 428 35 HOH HOH . I 6 HOH A 29 429 17 HOH HOH . I 6 HOH A 30 430 15 HOH HOH . I 6 HOH A 31 431 46 HOH HOH . I 6 HOH A 32 432 38 HOH HOH . I 6 HOH A 33 433 27 HOH HOH . I 6 HOH A 34 434 28 HOH HOH . I 6 HOH A 35 435 50 HOH HOH . I 6 HOH A 36 436 24 HOH HOH . I 6 HOH A 37 437 9 HOH HOH . I 6 HOH A 38 438 37 HOH HOH . I 6 HOH A 39 439 30 HOH HOH . I 6 HOH A 40 440 26 HOH HOH . I 6 HOH A 41 441 33 HOH HOH . I 6 HOH A 42 442 21 HOH HOH . I 6 HOH A 43 443 29 HOH HOH . I 6 HOH A 44 444 43 HOH HOH . I 6 HOH A 45 445 32 HOH HOH . I 6 HOH A 46 446 45 HOH HOH . I 6 HOH A 47 447 49 HOH HOH . I 6 HOH A 48 448 39 HOH HOH . I 6 HOH A 49 449 42 HOH HOH . I 6 HOH A 50 450 47 HOH HOH . I 6 HOH A 51 451 48 HOH HOH . I 6 HOH A 52 452 41 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 C01 N46 . A . B 2 -3.729 -5.858 15.361 0.2 31.54 ? C01 N46 301 A 1 HETATM 2 C C02 N46 . A . B 2 -3.491 -5.938 13.859 0.2 34.34 ? C02 N46 301 A 1 HETATM 3 C C03 N46 . A . B 2 -4.392 -6.867 13.044 0.2 36.71 ? C03 N46 301 A 1 HETATM 4 C C04 N46 . A . B 2 -5.829 -6.406 12.793 0.2 36.33 ? C04 N46 301 A 1 HETATM 5 C C06 N46 . A . B 2 -5.632 -5.051 12.115 0.2 36.82 ? C06 N46 301 A 1 HETATM 6 O O05 N46 . A . B 2 -6.484 -7.338 12.012 0.2 32.93 ? O05 N46 301 A 1 HETATM 7 O O07 N46 . A . B 2 -6.876 -4.602 11.709 0.2 34.02 ? O07 N46 301 A 1 HETATM 8 O O09 N46 . A . B 2 -5.994 -3.22 9.691 0.2 37.05 ? O09 N46 301 A 1 HETATM 9 O O10 N46 . A . B 2 -7.096 -5.405 9.261 0.2 34.14 ? O10 N46 301 A 1 HETATM 10 O O11 N46 . A . B 2 -8.439 -3.509 10.067 0.2 25.91 ? O11 N46 301 A 1 HETATM 11 O O12 N46 . A . B 2 -3.989 -7.884 12.574 0.2 39.09 ? O12 N46 301 A 1 HETATM 12 O O13 N46 . A . B 2 -2.655 -5.269 13.338 0.2 35.22 ? O13 N46 301 A 1 HETATM 13 P P08 N46 . A . B 2 -7.086 -4.173 10.134 0.2 27.55 ? P08 N46 301 A 1 HETATM 14 H H011 N46 . A . B 2 -4.356 -6.688 15.673 0.2 37.85 ? H011 N46 301 A 1 HETATM 15 H H012 N46 . A . B 2 -4.224 -4.921 15.6 0.2 37.85 ? H012 N46 301 A 1 HETATM 16 H H013 N46 . A . B 2 -2.778 -5.908 15.882 0.2 37.85 ? H013 N46 301 A 1 HETATM 17 H H041 N46 . A . B 2 -6.449 -6.314 13.676 0.2 43.6 ? H041 N46 301 A 1 HETATM 18 H H061 N46 . A . B 2 -5.197 -4.347 12.817 0.2 44.19 ? H061 N46 301 A 1 HETATM 19 H H062 N46 . A . B 2 -4.98 -5.16 11.255 0.2 44.19 ? H062 N46 301 A 1 HETATM 20 H H051 N46 . A . B 2 -6.705 -6.946 11.192 0.2 39.52 ? H051 N46 301 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #