data_5K5D # _model_server_result.job_id CTFj9-XPpZu2rj4bXMYZwQ _model_server_result.datetime_utc '2025-09-09 14:42:36' _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 5k5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 5K5D # _exptl.entry_id 5K5D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 192.124 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CITRIC ACID' _entity.pdbx_number_of_molecules 4 _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 5K5D _cell.length_a 71.03 _cell.length_b 98.7 _cell.length_c 307.2 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K5D _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,E,I 1 1 A,D,H 2 1 C,F,G,J 3 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 D N N ? 2 E N N ? 2 F N N ? 2 G 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 C MSE 4 B MSE 1 1_555 A N THR 5 B THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C THR 27 B THR 24 1_555 A N MSE 28 B MSE 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C MSE 28 B MSE 25 1_555 A N VAL 29 B VAL 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C ILE 68 B ILE 65 1_555 A N MSE 69 B MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C MSE 69 B MSE 66 1_555 A N LYS 70 B LYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 A C LYS 125 B LYS 122 1_555 A N MSE 126 B MSE 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C MSE 126 B MSE 123 1_555 A N GLN 127 B GLN 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 A C LYS 194 B LYS 191 1_555 A N MSE 195 B MSE 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale9 A C MSE 195 B MSE 192 1_555 A N ALA 196 B ALA 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 A C ASP 230 B ASP 227 1_555 A N MSE 231 B MSE 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale11 A C MSE 231 B MSE 228 1_555 A N GLY 232 B GLY 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 A C LEU 266 B LEU 263 1_555 A N MSE 267 B MSE 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale13 A C MSE 267 B MSE 264 1_555 A N GLU 268 B GLU 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale14 B C MSE 4 A MSE 1 1_555 B N THR 5 A THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale15 B C THR 27 A THR 24 1_555 B N MSE 28 A MSE 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale16 B C MSE 28 A MSE 25 1_555 B N VAL 29 A VAL 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 B C ILE 68 A ILE 65 1_555 B N MSE 69 A MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale18 B C MSE 69 A MSE 66 1_555 B N LYS 70 A LYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale19 B C LYS 125 A LYS 122 1_555 B N MSE 126 A MSE 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale20 B C MSE 126 A MSE 123 1_555 B N GLN 127 A GLN 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale21 B C LYS 194 A LYS 191 1_555 B N MSE 195 A MSE 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale22 B C MSE 195 A MSE 192 1_555 B N ALA 196 A ALA 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale23 B C ASP 230 A ASP 227 1_555 B N MSE 231 A MSE 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale24 B C MSE 231 A MSE 228 1_555 B N GLY 232 A GLY 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale25 B C LEU 266 A LEU 263 1_555 B N MSE 267 A MSE 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale26 B C MSE 267 A MSE 264 1_555 B N GLU 268 A GLU 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale27 C C MSE 4 C MSE 1 1_555 C N THR 5 C THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale28 C C THR 27 C THR 24 1_555 C N MSE 28 C MSE 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale29 C C MSE 28 C MSE 25 1_555 C N VAL 29 C VAL 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale30 C C ILE 68 C ILE 65 1_555 C N MSE 69 C MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale31 C C MSE 69 C MSE 66 1_555 C N LYS 70 C LYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale32 C C LYS 125 C LYS 122 1_555 C N MSE 126 C MSE 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale33 C C MSE 126 C MSE 123 1_555 C N GLN 127 C GLN 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale34 C C LYS 194 C LYS 191 1_555 C N MSE 195 C MSE 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale35 C C MSE 195 C MSE 192 1_555 C N ALA 196 C ALA 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale36 C C ASP 230 C ASP 227 1_555 C N MSE 231 C MSE 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale37 C C MSE 231 C MSE 228 1_555 C N GLY 232 C GLY 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale38 C C LEU 266 C LEU 263 1_555 C N MSE 267 C MSE 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale39 C C MSE 267 C MSE 264 1_555 C N GLU 268 C GLU 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _chem_comp.formula 'C6 H8 O7' _chem_comp.formula_weight 192.124 _chem_comp.id CIT _chem_comp.mon_nstd_flag . _chem_comp.name 'CITRIC ACID' _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 C1 O1 CIT doub 70 n n C1 O2 CIT sing 71 n n C1 C2 CIT sing 72 n n O2 HO2 CIT sing 73 n n C2 C3 CIT sing 74 n n C2 H21 CIT sing 75 n n C2 H22 CIT sing 76 n n C3 O7 CIT sing 77 n n C3 C4 CIT sing 78 n n C3 C6 CIT sing 79 n n O7 HO7 CIT sing 80 n n C4 C5 CIT sing 81 n n C4 H41 CIT sing 82 n n C4 H42 CIT sing 83 n n C5 O3 CIT doub 84 n n C5 O4 CIT sing 85 n n O4 HO4 CIT sing 86 n n C6 O5 CIT doub 87 n n C6 O6 CIT sing 88 n n O6 HO6 CIT sing 89 n n # _atom_sites.entry_id 5K5D _atom_sites.fract_transf_matrix[1][1] 0.014079 _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] 0.010132 _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] 0.003255 _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 D 2 CIT B 1 301 438 CIT CIT . E 2 CIT A 1 301 432 CIT CIT . F 2 CIT C 1 301 430 CIT CIT . G 2 CIT C 1 302 338 CIT CIT . H 3 HOH B 1 401 36 HOH HOH . H 3 HOH B 2 402 60 HOH HOH . H 3 HOH B 3 403 27 HOH HOH . H 3 HOH B 4 404 38 HOH HOH . H 3 HOH B 5 405 28 HOH HOH . H 3 HOH B 6 406 34 HOH HOH . H 3 HOH B 7 407 3 HOH HOH . H 3 HOH B 8 408 92 HOH HOH . H 3 HOH B 9 409 4 HOH HOH . H 3 HOH B 10 410 50 HOH HOH . H 3 HOH B 11 411 70 HOH HOH . H 3 HOH B 12 412 57 HOH HOH . H 3 HOH B 13 413 51 HOH HOH . H 3 HOH B 14 414 68 HOH HOH . H 3 HOH B 15 415 7 HOH HOH . H 3 HOH B 16 416 35 HOH HOH . H 3 HOH B 17 417 29 HOH HOH . H 3 HOH B 18 418 9 HOH HOH . H 3 HOH B 19 419 89 HOH HOH . H 3 HOH B 20 420 88 HOH HOH . H 3 HOH B 21 421 10 HOH HOH . H 3 HOH B 22 422 44 HOH HOH . H 3 HOH B 23 423 48 HOH HOH . H 3 HOH B 24 424 39 HOH HOH . H 3 HOH B 25 425 42 HOH HOH . H 3 HOH B 26 426 61 HOH HOH . H 3 HOH B 27 427 67 HOH HOH . H 3 HOH B 28 428 102 HOH HOH . H 3 HOH B 29 429 81 HOH HOH . H 3 HOH B 30 430 99 HOH HOH . H 3 HOH B 31 431 20 HOH HOH . H 3 HOH B 32 432 80 HOH HOH . H 3 HOH B 33 433 16 HOH HOH . H 3 HOH B 34 434 24 HOH HOH . H 3 HOH B 35 435 78 HOH HOH . H 3 HOH B 36 436 41 HOH HOH . H 3 HOH B 37 437 56 HOH HOH . H 3 HOH B 38 438 22 HOH HOH . H 3 HOH B 39 439 52 HOH HOH . H 3 HOH B 40 440 46 HOH HOH . H 3 HOH B 41 441 21 HOH HOH . I 3 HOH A 1 401 90 HOH HOH . I 3 HOH A 2 402 11 HOH HOH . I 3 HOH A 3 403 32 HOH HOH . I 3 HOH A 4 404 30 HOH HOH . I 3 HOH A 5 405 13 HOH HOH . I 3 HOH A 6 406 64 HOH HOH . I 3 HOH A 7 407 15 HOH HOH . I 3 HOH A 8 408 33 HOH HOH . I 3 HOH A 9 409 45 HOH HOH . I 3 HOH A 10 410 103 HOH HOH . I 3 HOH A 11 411 65 HOH HOH . I 3 HOH A 12 412 74 HOH HOH . I 3 HOH A 13 413 1 HOH HOH . I 3 HOH A 14 414 101 HOH HOH . I 3 HOH A 15 415 6 HOH HOH . I 3 HOH A 16 416 8 HOH HOH . I 3 HOH A 17 417 59 HOH HOH . I 3 HOH A 18 418 77 HOH HOH . I 3 HOH A 19 419 37 HOH HOH . I 3 HOH A 20 420 40 HOH HOH . I 3 HOH A 21 421 85 HOH HOH . I 3 HOH A 22 422 54 HOH HOH . I 3 HOH A 23 423 43 HOH HOH . I 3 HOH A 24 424 96 HOH HOH . I 3 HOH A 25 425 19 HOH HOH . I 3 HOH A 26 426 71 HOH HOH . I 3 HOH A 27 427 69 HOH HOH . I 3 HOH A 28 428 2 HOH HOH . I 3 HOH A 29 429 18 HOH HOH . I 3 HOH A 30 430 66 HOH HOH . I 3 HOH A 31 431 87 HOH HOH . I 3 HOH A 32 432 98 HOH HOH . I 3 HOH A 33 433 75 HOH HOH . I 3 HOH A 34 434 104 HOH HOH . I 3 HOH A 35 435 72 HOH HOH . I 3 HOH A 36 436 73 HOH HOH . I 3 HOH A 37 437 17 HOH HOH . I 3 HOH A 38 438 5 HOH HOH . I 3 HOH A 39 439 105 HOH HOH . I 3 HOH A 40 440 82 HOH HOH . I 3 HOH A 41 441 25 HOH HOH . I 3 HOH A 42 442 94 HOH HOH . I 3 HOH A 43 443 91 HOH HOH . I 3 HOH A 44 444 86 HOH HOH . J 3 HOH C 1 401 31 HOH HOH . J 3 HOH C 2 402 58 HOH HOH . J 3 HOH C 3 403 26 HOH HOH . J 3 HOH C 4 404 95 HOH HOH . J 3 HOH C 5 405 12 HOH HOH . J 3 HOH C 6 406 76 HOH HOH . J 3 HOH C 7 407 23 HOH HOH . J 3 HOH C 8 408 47 HOH HOH . J 3 HOH C 9 409 84 HOH HOH . J 3 HOH C 10 410 62 HOH HOH . J 3 HOH C 11 411 14 HOH HOH . J 3 HOH C 12 412 79 HOH HOH . J 3 HOH C 13 413 49 HOH HOH . J 3 HOH C 14 414 100 HOH HOH . J 3 HOH C 15 415 97 HOH HOH . J 3 HOH C 16 416 55 HOH HOH . J 3 HOH C 17 417 53 HOH HOH . J 3 HOH C 18 418 63 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 CIT . . . F 2 -49.416 -7.564 6.102 1 76.77 ? C1 CIT 301 C 1 HETATM 2 O O1 CIT . . . F 2 -49.345 -8.781 5.837 1 78.84 ? O1 CIT 301 C 1 HETATM 3 O O2 CIT . . . F 2 -48.529 -6.789 5.683 1 74.29 ? O2 CIT 301 C 1 HETATM 4 C C2 CIT . . . F 2 -50.574 -7.036 6.906 1 78.59 ? C2 CIT 301 C 1 HETATM 5 C C3 CIT . . . F 2 -51.831 -7.792 6.5 1 80.36 ? C3 CIT 301 C 1 HETATM 6 O O7 CIT . . . F 2 -51.842 -7.975 5.062 1 74.95 ? O7 CIT 301 C 1 HETATM 7 C C4 CIT . . . F 2 -53.084 -7.036 6.936 1 80.08 ? C4 CIT 301 C 1 HETATM 8 C C5 CIT . . . F 2 -53.308 -5.841 6.036 1 82.08 ? C5 CIT 301 C 1 HETATM 9 O O3 CIT . . . F 2 -52.866 -4.712 6.35 1 84.64 ? O3 CIT 301 C 1 HETATM 10 O O4 CIT . . . F 2 -53.948 -5.965 4.968 1 75.83 ? O4 CIT 301 C 1 HETATM 11 C C6 CIT . . . F 2 -51.779 -9.164 7.147 1 85.16 ? C6 CIT 301 C 1 HETATM 12 O O5 CIT . . . F 2 -52.003 -10.189 6.467 1 88.38 ? O5 CIT 301 C 1 HETATM 13 O O6 CIT . . . F 2 -51.487 -9.279 8.356 1 82.91 ? O6 CIT 301 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 13 #