data_5DYH # _model_server_result.job_id bbSeqQANww3-vWR1zBVOMw _model_server_result.datetime_utc '2024-11-22 22:38:49' _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 5dyh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 5DYH # _exptl.entry_id 5DYH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 192.124 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'CITRIC ACID' _entity.pdbx_number_of_molecules 11 _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 5DYH _cell.length_a 88.275 _cell.length_b 102.016 _cell.length_c 197.899 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DYH _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J 1 1 B,K,L,M,N,O,P,Q 2 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 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O 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 disulf ? disulf1 A SG CYS 28 A CYS 9 1_555 A SG CYS 67 A CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 38 A CYS 19 1_555 A SG CYS 58 A CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 137 A CYS 118 1_555 A SG CYS 213 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 156 A CYS 137 1_555 A SG CYS 350 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 177 A CYS 158 1_555 A SG CYS 193 A CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 A SG CYS 180 A CYS 161 1_555 A SG CYS 198 A CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 190 A CYS 171 1_555 A SG CYS 196 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 A SG CYS 246 A CYS 227 1_555 A SG CYS 260 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 A SG CYS 358 A CYS 339 1_555 A SG CYS 615 A CYS 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 A SG CYS 364 A CYS 345 1_555 A SG CYS 396 A CYS 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf11 A SG CYS 374 A CYS 355 1_555 A SG CYS 387 A CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 A SG CYS 421 A CYS 402 1_555 A SG CYS 693 A CYS 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 A SG CYS 437 A CYS 418 1_555 A SG CYS 656 A CYS 637 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf14 A SG CYS 469 A CYS 450 1_555 A SG CYS 542 A CYS 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 A SG CYS 493 A CYS 474 1_555 A SG CYS 684 A CYS 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 A SG CYS 503 A CYS 484 1_555 A SG CYS 517 A CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf17 A SG CYS 514 A CYS 495 1_555 A SG CYS 525 A CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf18 A SG CYS 582 A CYS 563 1_555 A SG CYS 596 A CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf19 A SG CYS 634 A CYS 615 1_555 A SG CYS 639 A CYS 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf20 B SG CYS 28 B CYS 9 1_555 B SG CYS 67 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf21 B SG CYS 38 B CYS 19 1_555 B SG CYS 58 B CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf22 B SG CYS 137 B CYS 118 1_555 B SG CYS 213 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf23 B SG CYS 156 B CYS 137 1_555 B SG CYS 350 B CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf24 B SG CYS 177 B CYS 158 1_555 B SG CYS 193 B CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf25 B SG CYS 180 B CYS 161 1_555 B SG CYS 198 B CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf26 B SG CYS 190 B CYS 171 1_555 B SG CYS 196 B CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf27 B SG CYS 246 B CYS 227 1_555 B SG CYS 260 B CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf28 B SG CYS 358 B CYS 339 1_555 B SG CYS 615 B CYS 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf29 B SG CYS 364 B CYS 345 1_555 B SG CYS 396 B CYS 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf30 B SG CYS 374 B CYS 355 1_555 B SG CYS 387 B CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf31 B SG CYS 421 B CYS 402 1_555 B SG CYS 693 B CYS 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf32 B SG CYS 437 B CYS 418 1_555 B SG CYS 656 B CYS 637 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf33 B SG CYS 469 B CYS 450 1_555 B SG CYS 542 B CYS 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf34 B SG CYS 493 B CYS 474 1_555 B SG CYS 684 B CYS 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf35 B SG CYS 503 B CYS 484 1_555 B SG CYS 517 B CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf36 B SG CYS 514 B CYS 495 1_555 B SG CYS 525 B CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf37 B SG CYS 582 B CYS 563 1_555 B SG CYS 596 B CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf38 B SG CYS 634 B CYS 615 1_555 B SG CYS 639 B CYS 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? # _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 5DYH _atom_sites.fract_transf_matrix[1][1] 0.011328 _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] 0.009802 _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] 0.005053 _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 CIT A 1 701 12 CIT CIT . D 2 CIT A 1 702 17 CIT CIT . E 2 CIT A 1 703 19 CIT CIT . F 2 CIT A 1 704 20 CIT CIT . G 2 CIT A 1 705 21 CIT CIT . H 2 CIT A 1 706 22 CIT CIT . I 3 4TI A 1 707 1 4TI TI . J 4 CO3 A 1 708 1 CO3 CO3 . K 2 CIT B 1 701 13 CIT CIT . L 2 CIT B 1 702 14 CIT CIT . M 2 CIT B 1 703 15 CIT CIT . N 2 CIT B 1 704 16 CIT CIT . O 2 CIT B 1 705 18 CIT CIT . P 3 4TI B 1 706 2 4TI TI . Q 4 CO3 B 1 707 1 CO3 CO3 . # 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 . . . C 2 3.514 0.697 -23.185 1 153.01 ? C1 CIT 701 A 1 HETATM 2 O O1 CIT . . . C 2 3.321 1.071 -24.371 1 160.6 ? O1 CIT 701 A 1 HETATM 3 O O2 CIT . . . C 2 2.772 1.129 -22.265 1 161.49 ? O2 CIT 701 A 1 HETATM 4 C C2 CIT . . . C 2 4.635 -0.266 -22.863 1 156.27 ? C2 CIT 701 A 1 HETATM 5 C C3 CIT . . . C 2 5.568 -0.388 -24.049 1 161.3 ? C3 CIT 701 A 1 HETATM 6 O O7 CIT . . . C 2 5.57 0.825 -24.763 1 167.94 ? O7 CIT 701 A 1 HETATM 7 C C4 CIT . . . C 2 5.063 -1.505 -24.942 1 181.51 ? C4 CIT 701 A 1 HETATM 8 C C5 CIT . . . C 2 5.829 -1.567 -26.249 1 184.4 ? C5 CIT 701 A 1 HETATM 9 O O3 CIT . . . C 2 5.545 -2.451 -27.1 1 179.58 ? O3 CIT 701 A 1 HETATM 10 O O4 CIT . . . C 2 6.745 -0.738 -26.495 1 185.93 ? O4 CIT 701 A 1 HETATM 11 C C6 CIT . . . C 2 6.969 -0.69 -23.548 1 158.61 ? C6 CIT 701 A 1 HETATM 12 O O5 CIT . . . C 2 7.602 -1.696 -23.967 1 142.43 ? O5 CIT 701 A 1 HETATM 13 O O6 CIT . . . C 2 7.511 0.067 -22.701 1 167.25 ? O6 CIT 701 A 1 HETATM 14 H H21 CIT . . . C 2 5.135 0.065 -22.09 1 162.87 ? H21 CIT 701 A 1 HETATM 15 H H22 CIT . . . C 2 4.259 -1.144 -22.654 1 162.87 ? H22 CIT 701 A 1 HETATM 16 H H41 CIT . . . C 2 4.116 -1.355 -25.134 1 192.39 ? H41 CIT 701 A 1 HETATM 17 H H42 CIT . . . C 2 5.163 -2.357 -24.473 1 192.39 ? H42 CIT 701 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 17 #