data_4ZDA # _model_server_result.job_id Qh0txKC-cHWrCioYWRgh8g _model_server_result.datetime_utc '2024-10-28 02:32:20' _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 4zda # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":802}' # _entry.id 4ZDA # _exptl.entry_id 4ZDA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 192.124 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ISOCITRIC ACID' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.97 _cell.angle_gamma 90 _cell.entry_id 4ZDA _cell.length_a 201.774 _cell.length_b 206.162 _cell.length_c 145.598 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZDA _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R _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 ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R 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 metalc ? metalc1 A OD2 ASP 352 A ASP 352 1_555 G MN MN . A MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc2 A OD1 ASP 551 A ASP 551 1_555 G MN MN . A MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc3 A OD2 ASP 555 A ASP 555 1_555 G MN MN . A MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc4 G MN MN . A MN 801 1_555 H O1 ICT . A ICT 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc5 G MN MN . A MN 801 1_555 H O7 ICT . A ICT 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc6 B OD2 ASP 352 B ASP 352 1_555 I MN MN . B MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc7 B OD1 ASP 551 B ASP 551 1_555 I MN MN . B MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc8 B OD2 ASP 555 B ASP 555 1_555 I MN MN . B MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc9 I MN MN . B MN 801 1_555 J O7 ICT . B ICT 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc10 C OD2 ASP 352 C ASP 352 1_555 K MN MN . C MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc11 C OD1 ASP 551 C ASP 551 1_555 K MN MN . C MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc12 C OD2 ASP 555 C ASP 555 1_555 K MN MN . C MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc13 K MN MN . C MN 801 1_555 L O2 ICT . C ICT 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc14 K MN MN . C MN 801 1_555 L O7 ICT . C ICT 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc15 D OD2 ASP 352 D ASP 352 1_555 M MN MN . D MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc16 D OD1 ASP 551 D ASP 551 1_555 M MN MN . D MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc17 D OD2 ASP 555 D ASP 555 1_555 M MN MN . D MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc18 M MN MN . D MN 801 1_555 N O7 ICT . D ICT 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc19 E OD2 ASP 352 E ASP 352 1_555 O MN MN . E MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc20 E OD1 ASP 551 E ASP 551 1_555 O MN MN . E MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc21 E OD2 ASP 555 E ASP 555 1_555 O MN MN . E MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc22 O MN MN . E MN 801 1_555 P O7 ICT . E ICT 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc23 O MN MN . E MN 801 1_555 P O1 ICT . E ICT 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc24 F OD2 ASP 352 F ASP 352 1_555 Q MN MN . F MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc25 F OD1 ASP 551 F ASP 551 1_555 Q MN MN . F MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc26 F OD2 ASP 555 F ASP 555 1_555 Q MN MN . F MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc27 Q MN MN . F MN 801 1_555 R O7 ICT . F ICT 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? # _chem_comp.formula 'C6 H8 O7' _chem_comp.formula_weight 192.124 _chem_comp.id ICT _chem_comp.mon_nstd_flag . _chem_comp.name 'ISOCITRIC 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 ICT doub 150 n n C1 O2 ICT sing 151 n n C1 C2 ICT sing 152 n n O2 HO2 ICT sing 153 n n C2 O7 ICT sing 154 n n C2 C3 ICT sing 155 n n C2 H2 ICT sing 156 n n O7 HO7 ICT sing 157 n n C3 C4 ICT sing 158 n n C3 C6 ICT sing 159 n n C3 H3 ICT sing 160 n n C4 C5 ICT sing 161 n n C4 H41 ICT sing 162 n n C4 H42 ICT sing 163 n n C5 O3 ICT doub 164 n n C5 O4 ICT sing 165 n n O4 HO4 ICT sing 166 n n C6 O5 ICT doub 167 n n C6 O6 ICT sing 168 n n O6 HO6 ICT sing 169 n n # _atom_sites.entry_id 4ZDA _atom_sites.fract_transf_matrix[1][1] 0.004956 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000084 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004851 _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] 0.006869 _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 G 2 MN A 1 801 742 MN MN . H 3 ICT A 1 802 743 ICT ICT . I 2 MN B 1 801 742 MN MN . J 3 ICT B 1 802 743 ICT ICT . K 2 MN C 1 801 742 MN MN . L 3 ICT C 1 802 743 ICT ICT . M 2 MN D 1 801 742 MN MN . N 3 ICT D 1 802 743 ICT ICT . O 2 MN E 1 801 742 MN MN . P 3 ICT E 1 802 743 ICT ICT . Q 2 MN F 1 801 742 MN MN . R 3 ICT F 1 802 743 ICT ICT . # 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 ICT . . . R 3 47.22 26.807 -3.449 1 76.42 ? C1 ICT 802 F 1 HETATM 2 O O1 ICT . . . R 3 46.165 27.061 -4.07 1 78.6 ? O1 ICT 802 F 1 HETATM 3 O O2 ICT . . . R 3 47.257 26.582 -2.219 1 74.15 ? O2 ICT 802 F 1 HETATM 4 C C2 ICT . . . R 3 48.499 26.771 -4.23 1 75.38 ? C2 ICT 802 F 1 HETATM 5 O O7 ICT . . . R 3 49.426 25.88 -3.6 1 76.95 ? O7 ICT 802 F 1 HETATM 6 C C3 ICT . . . R 3 49.083 28.179 -4.331 1 75.53 ? C3 ICT 802 F 1 HETATM 7 C C4 ICT . . . R 3 49.939 28.289 -5.596 1 77.35 ? C4 ICT 802 F 1 HETATM 8 C C5 ICT . . . R 3 50.318 29.71 -5.97 1 79.27 ? C5 ICT 802 F 1 HETATM 9 O O3 ICT . . . R 3 51.084 29.861 -6.947 1 79.04 ? O3 ICT 802 F 1 HETATM 10 O O4 ICT . . . R 3 49.872 30.683 -5.315 1 80.85 ? O4 ICT 802 F 1 HETATM 11 C C6 ICT . . . R 3 49.865 28.518 -3.087 1 73.26 ? C6 ICT 802 F 1 HETATM 12 O O5 ICT . . . R 3 51.102 28.341 -3.073 1 72.69 ? O5 ICT 802 F 1 HETATM 13 O O6 ICT . . . R 3 49.246 28.966 -2.1 1 70.53 ? O6 ICT 802 F 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 112 _model_server_stats.query_time_ms 375 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 13 #