data_5X0I # _model_server_result.job_id 4jOYmpquYoUOQbiY5-u6aA _model_server_result.datetime_utc '2024-11-24 04:39:06' _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 5x0i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":603}' # _entry.id 5X0I # _exptl.entry_id 5X0I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.062 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYRUVIC 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 5X0I _cell.length_a 116.601 _cell.length_b 137.875 _cell.length_c 149.709 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X0I _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA _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 ? 4 G N N ? 4 L N N ? 4 Q N N ? 4 V 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 OD1 ASN 95 A ASN 75 1_555 I K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc2 A OG SER 97 A SER 77 1_555 I K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc3 A OD1 ASP 133 A ASP 113 1_555 I K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc4 A O THR 134 A THR 114 1_555 I K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc5 A OE1 GLU 292 A GLU 272 1_555 H MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc6 A OD2 ASP 316 A ASP 296 1_555 H MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc7 G OXT PYR . A PYR 603 1_555 H MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc8 G O3 PYR . A PYR 603 1_555 H MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc9 B OD1 ASN 95 B ASN 75 1_555 N K K . B K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc10 B OG SER 97 B SER 77 1_555 N K K . B K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.958 ? metalc ? metalc11 B OD1 ASP 133 B ASP 113 1_555 N K K . B K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc12 B O THR 134 B THR 114 1_555 N K K . B K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc13 B OE1 GLU 292 B GLU 272 1_555 M MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc14 B OD2 ASP 316 B ASP 296 1_555 M MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc15 L OXT PYR . B PYR 603 1_555 M MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc16 L O3 PYR . B PYR 603 1_555 M MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc17 N K K . B K 605 1_555 Z O HOH . B HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc18 C OD1 ASN 95 C ASN 75 1_555 S K K . C K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc19 C OG SER 97 C SER 77 1_555 S K K . C K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc20 C OD1 ASP 133 C ASP 113 1_555 S K K . C K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? metalc ? metalc21 C O THR 134 C THR 114 1_555 S K K . C K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc22 C OE1 GLU 292 C GLU 272 1_555 R MG MG . C MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc23 C OD2 ASP 316 C ASP 296 1_555 R MG MG . C MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc24 Q O PYR . C PYR 603 1_555 R MG MG . C MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc25 Q O3 PYR . C PYR 603 1_555 R MG MG . C MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.735 ? metalc ? metalc26 D OD1 ASN 95 D ASN 75 1_555 X K K . D K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc27 D OG SER 97 D SER 77 1_555 X K K . D K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc28 D OD1 ASP 133 D ASP 113 1_555 X K K . D K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc29 D O THR 134 D THR 114 1_555 X K K . D K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? metalc ? metalc30 D OE1 GLU 292 D GLU 272 1_555 W MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc31 D OD2 ASP 316 D ASP 296 1_555 W MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc32 V O3 PYR . D PYR 603 1_555 W MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? # _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 311 n n C OXT PYR sing 312 n n C CA PYR sing 313 n n OXT HXT PYR sing 314 n n CA O3 PYR doub 315 n n CA CB PYR sing 316 n n CB HB1 PYR sing 317 n n CB HB2 PYR sing 318 n n CB HB3 PYR sing 319 n n # _atom_sites.entry_id 5X0I _atom_sites.fract_transf_matrix[1][1] 0.008576 _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] 0.007253 _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] 0.00668 _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 FBP A 1 601 540 FBP FBP . F 3 SER A 1 602 542 SER SER . G 4 PYR A 1 603 545 PYR PYR . H 5 MG A 1 604 546 MG MG . I 6 K A 1 605 547 K K . J 2 FBP B 1 601 540 FBP FBP . K 3 SER B 1 602 542 SER SER . L 4 PYR B 1 603 545 PYR PYR . M 5 MG B 1 604 546 MG MG . N 6 K B 1 605 547 K K . O 2 FBP C 1 601 540 FBP FBP . P 3 SER C 1 602 542 SER SER . Q 4 PYR C 1 603 545 PYR PYR . R 5 MG C 1 604 546 MG MG . S 6 K C 1 605 547 K K . T 2 FBP D 1 601 540 FBP FBP . U 3 SER D 1 602 542 SER SER . V 4 PYR D 1 603 545 PYR PYR . W 5 MG D 1 604 546 MG MG . X 6 K D 1 605 547 K K . Y 7 HOH A 1 701 84 HOH HOH . Y 7 HOH A 2 702 93 HOH HOH . Y 7 HOH A 3 703 32 HOH HOH . Y 7 HOH A 4 704 87 HOH HOH . Y 7 HOH A 5 705 11 HOH HOH . Y 7 HOH A 6 706 9 HOH HOH . Y 7 HOH A 7 707 62 HOH HOH . Y 7 HOH A 8 708 63 HOH HOH . Y 7 HOH A 9 709 115 HOH HOH . Y 7 HOH A 10 710 90 HOH HOH . Y 7 HOH A 11 711 64 HOH HOH . Y 7 HOH A 12 712 77 HOH HOH . Y 7 HOH A 13 713 61 HOH HOH . Z 7 HOH B 1 701 97 HOH HOH . Z 7 HOH B 2 702 80 HOH HOH . Z 7 HOH B 3 703 71 HOH HOH . Z 7 HOH B 4 704 26 HOH HOH . Z 7 HOH B 5 705 34 HOH HOH . Z 7 HOH B 6 706 5 HOH HOH . Z 7 HOH B 7 707 103 HOH HOH . Z 7 HOH B 8 708 81 HOH HOH . Z 7 HOH B 9 709 114 HOH HOH . Z 7 HOH B 10 710 65 HOH HOH . Z 7 HOH B 11 711 83 HOH HOH . Z 7 HOH B 12 712 69 HOH HOH . Z 7 HOH B 13 713 70 HOH HOH . AA 7 HOH C 1 701 120 HOH HOH . AA 7 HOH C 2 702 72 HOH HOH . AA 7 HOH C 3 703 3 HOH HOH . AA 7 HOH C 4 704 1 HOH HOH . AA 7 HOH C 5 705 116 HOH HOH . AA 7 HOH C 6 706 8 HOH HOH . AA 7 HOH C 7 707 85 HOH HOH . AA 7 HOH C 8 708 60 HOH HOH . AA 7 HOH C 9 709 67 HOH HOH . BA 7 HOH D 1 701 66 HOH HOH . BA 7 HOH D 2 702 88 HOH HOH . BA 7 HOH D 3 703 105 HOH HOH . BA 7 HOH D 4 704 10 HOH HOH . BA 7 HOH D 5 705 98 HOH HOH . BA 7 HOH D 6 706 6 HOH HOH . BA 7 HOH D 7 707 17 HOH HOH . BA 7 HOH D 8 708 27 HOH HOH . BA 7 HOH D 9 709 74 HOH HOH . BA 7 HOH D 10 710 75 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 . . . L 4 38.578 -5.713 -9.651 1 32.05 ? C PYR 603 B 1 HETATM 2 O O PYR . . . L 4 38.395 -5.141 -8.538 1 35.02 ? O PYR 603 B 1 HETATM 3 O OXT PYR . . . L 4 38.269 -6.94 -9.897 1 30.61 ? OXT PYR 603 B 1 HETATM 4 C CA PYR . . . L 4 39.218 -4.956 -10.711 1 25.82 ? CA PYR 603 B 1 HETATM 5 O O3 PYR . . . L 4 39.21 -5.508 -11.779 1 25.24 ? O3 PYR 603 B 1 HETATM 6 C CB PYR . . . L 4 39.89 -3.633 -10.445 1 24.01 ? CB PYR 603 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 228 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 6 #