data_4JX6 # _model_server_result.job_id NvWa24Y84cd5I9ctrcUtsg _model_server_result.datetime_utc '2024-12-02 18:31:08' _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 4jx6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1101}' # _entry.id 4JX6 # _exptl.entry_id 4JX6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.062 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYRUVIC ACID' _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 90 _cell.angle_gamma 90 _cell.entry_id 4JX6 _cell.length_a 84.809 _cell.length_b 157.28 _cell.length_c 245.885 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JX6 _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 ? tetrameric 4 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 1 1 A,C,E,F,G,K,L,M,P,R 2 1 B,D,H,I,J,N,O,Q,S 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 E N N ? 2 H 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 VAL 282 A VAL 717 1_555 A N KCX 283 A KCX 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C KCX 283 A KCX 718 1_555 A N ASP 284 A ASP 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 B C VAL 282 B VAL 717 1_555 B N KCX 283 B KCX 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 B C KCX 283 B KCX 718 1_555 B N ASP 284 B ASP 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 C C VAL 282 C VAL 717 1_555 C N KCX 283 C KCX 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 C C KCX 283 C KCX 718 1_555 C N ASP 284 C ASP 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale7 D C VAL 282 D VAL 717 1_555 D N KCX 283 D KCX 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale8 D C KCX 283 D KCX 718 1_555 D N ASP 284 D ASP 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? metalc ? metalc1 A O MET 99 A MET 534 1_555 G MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc2 A O ARG 100 A ARG 535 1_555 G MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc3 A O GLU 102 A GLU 537 1_555 G MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? metalc ? metalc4 A OD2 ASP 114 A ASP 549 1_555 F ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc5 A OQ2 KCX 283 A KCX 718 1_555 F ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc6 A OQ1 KCX 283 A KCX 718 1_555 F ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc7 A NE2 HIS 312 A HIS 747 1_555 F ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc8 A NE2 HIS 314 A HIS 749 1_555 F ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc9 A OD1 ASP 333 A ASP 768 1_555 G MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc10 F ZN ZN . A ZN 1102 1_555 P O HOH . A HOH 1223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc11 B O MET 99 B MET 534 1_555 J MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc12 B O ARG 100 B ARG 535 1_555 J MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc13 B O GLU 102 B GLU 537 1_555 J MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc14 B OD2 ASP 114 B ASP 549 1_555 I ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc15 B OQ1 KCX 283 B KCX 718 1_555 I ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc16 B OQ2 KCX 283 B KCX 718 1_555 I ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc17 B NE2 HIS 312 B HIS 747 1_555 I ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc18 B NE2 HIS 314 B HIS 749 1_555 I ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc19 B OD1 ASP 333 B ASP 768 1_555 J MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc20 I ZN ZN . B ZN 1102 1_555 Q O HOH . B HOH 1208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc21 J MG MG . B MG 1103 1_555 Q O HOH . B HOH 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc22 J MG MG . B MG 1103 1_555 Q O HOH . B HOH 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc23 C O MET 99 C MET 534 1_555 M MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc24 C O ARG 100 C ARG 535 1_555 M MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc25 C O GLU 102 C GLU 537 1_555 M MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc26 C OD2 ASP 114 C ASP 549 1_555 L ZN ZN . C ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc27 C OQ2 KCX 283 C KCX 718 1_555 L ZN ZN . C ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc28 C OQ1 KCX 283 C KCX 718 1_555 L ZN ZN . C ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc29 C NE2 HIS 312 C HIS 747 1_555 L ZN ZN . C ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc30 C NE2 HIS 314 C HIS 749 1_555 L ZN ZN . C ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc31 C OD1 ASP 333 C ASP 768 1_555 M MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc32 M MG MG . C MG 1103 1_555 R O HOH . C HOH 1212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc33 D O MET 99 D MET 534 1_555 O MG MG . D MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? metalc ? metalc34 D O ARG 100 D ARG 535 1_555 O MG MG . D MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc35 D O GLU 102 D GLU 537 1_555 O MG MG . D MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc36 D OD2 ASP 114 D ASP 549 1_555 N ZN ZN . D ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc37 D OQ1 KCX 283 D KCX 718 1_555 N ZN ZN . D ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc38 D NE2 HIS 312 D HIS 747 1_555 N ZN ZN . D ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc39 D NE2 HIS 314 D HIS 749 1_555 N ZN ZN . D ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc40 D OD1 ASP 333 D ASP 768 1_555 O MG MG . D MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? metalc ? metalc41 O MG MG . D MG 1102 1_555 S O HOH . D HOH 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc42 O MG MG . D MG 1102 1_555 S O HOH . D HOH 1208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? # _chem_comp.formula 'C3 H4 O3' _chem_comp.formula_weight 88.062 _chem_comp.id PYR _chem_comp.mon_nstd_flag . _chem_comp.name 'PYRUVIC 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 C O PYR doub 316 n n C OXT PYR sing 317 n n C CA PYR sing 318 n n OXT HXT PYR sing 319 n n CA O3 PYR doub 320 n n CA CB PYR sing 321 n n CB HB1 PYR sing 322 n n CB HB2 PYR sing 323 n n CB HB3 PYR sing 324 n n # _atom_sites.entry_id 4JX6 _atom_sites.fract_transf_matrix[1][1] 0.011791 _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] 0.006358 _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] 0.004067 _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 E 2 PYR A 1 1101 1101 PYR PYR . F 3 ZN A 1 1102 1102 ZN ZN . G 4 MG A 1 1103 1103 MG MG . H 2 PYR B 1 1101 1101 PYR PYR . I 3 ZN B 1 1102 1102 ZN ZN . J 4 MG B 1 1103 1103 MG MG . K 5 GOL C 1 1101 1104 GOL GOL . L 3 ZN C 1 1102 1101 ZN ZN . M 4 MG C 1 1103 1102 MG MG . N 3 ZN D 1 1101 1101 ZN ZN . O 4 MG D 1 1102 1102 MG MG . P 6 HOH A 1 1201 1201 HOH HOH . P 6 HOH A 2 1202 1202 HOH HOH . P 6 HOH A 3 1203 1203 HOH HOH . P 6 HOH A 4 1204 1204 HOH HOH . P 6 HOH A 5 1205 1205 HOH HOH . P 6 HOH A 6 1206 1206 HOH HOH . P 6 HOH A 7 1207 1207 HOH HOH . P 6 HOH A 8 1208 1208 HOH HOH . P 6 HOH A 9 1209 1209 HOH HOH . P 6 HOH A 10 1210 1210 HOH HOH . P 6 HOH A 11 1211 1211 HOH HOH . P 6 HOH A 12 1212 1212 HOH HOH . P 6 HOH A 13 1213 1213 HOH HOH . P 6 HOH A 14 1214 1214 HOH HOH . P 6 HOH A 15 1215 1215 HOH HOH . P 6 HOH A 16 1216 1216 HOH HOH . P 6 HOH A 17 1217 1217 HOH HOH . P 6 HOH A 18 1218 1218 HOH HOH . P 6 HOH A 19 1219 1219 HOH HOH . P 6 HOH A 20 1220 1220 HOH HOH . P 6 HOH A 21 1221 1221 HOH HOH . P 6 HOH A 22 1222 1222 HOH HOH . P 6 HOH A 23 1223 1223 HOH HOH . P 6 HOH A 24 1224 1224 HOH HOH . P 6 HOH A 25 1225 1225 HOH HOH . P 6 HOH A 26 1226 1226 HOH HOH . P 6 HOH A 27 1227 1227 HOH HOH . P 6 HOH A 28 1228 1203 HOH HOH . Q 6 HOH B 1 1201 1201 HOH HOH . Q 6 HOH B 2 1202 1202 HOH HOH . Q 6 HOH B 3 1203 1203 HOH HOH . Q 6 HOH B 4 1204 1204 HOH HOH . Q 6 HOH B 5 1205 1205 HOH HOH . Q 6 HOH B 6 1206 1206 HOH HOH . Q 6 HOH B 7 1207 1207 HOH HOH . Q 6 HOH B 8 1208 1208 HOH HOH . Q 6 HOH B 9 1209 1209 HOH HOH . Q 6 HOH B 10 1210 1210 HOH HOH . Q 6 HOH B 11 1211 1211 HOH HOH . Q 6 HOH B 12 1212 1212 HOH HOH . R 6 HOH C 1 1201 1201 HOH HOH . R 6 HOH C 2 1202 1202 HOH HOH . R 6 HOH C 3 1203 1204 HOH HOH . R 6 HOH C 4 1204 1205 HOH HOH . R 6 HOH C 5 1205 1206 HOH HOH . R 6 HOH C 6 1206 1207 HOH HOH . R 6 HOH C 7 1207 1208 HOH HOH . R 6 HOH C 8 1208 1209 HOH HOH . R 6 HOH C 9 1209 1210 HOH HOH . R 6 HOH C 10 1210 1211 HOH HOH . R 6 HOH C 11 1211 1212 HOH HOH . R 6 HOH C 12 1212 1213 HOH HOH . S 6 HOH D 1 1201 1201 HOH HOH . S 6 HOH D 2 1202 1202 HOH HOH . S 6 HOH D 3 1203 1203 HOH HOH . S 6 HOH D 4 1204 1204 HOH HOH . S 6 HOH D 5 1205 1205 HOH HOH . S 6 HOH D 6 1206 1206 HOH HOH . S 6 HOH D 7 1207 1207 HOH HOH . S 6 HOH D 8 1208 1208 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 C PYR . . . H 2 -80.539 15.82 -22.076 1 88.84 ? C PYR 1101 B 1 HETATM 2 O O PYR . . . H 2 -81.246 15.556 -21.068 1 91.92 ? O PYR 1101 B 1 HETATM 3 O OXT PYR . . . H 2 -80.89 15.422 -23.223 1 80.04 ? OXT PYR 1101 B 1 HETATM 4 C CA PYR . . . H 2 -79.282 16.589 -21.9 1 81.47 ? CA PYR 1101 B 1 HETATM 5 O O3 PYR . . . H 2 -78.237 16.137 -22.338 1 74.3 ? O3 PYR 1101 B 1 HETATM 6 C CB PYR . . . H 2 -79.276 17.913 -21.184 1 76.66 ? CB PYR 1101 B 1 # _model_server_stats.io_time_ms 111 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 389 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #