data_5JVL # _model_server_result.job_id cBhVCsWmv1NMQKRnw6i0fA _model_server_result.datetime_utc '2025-08-31 07:19:10' _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 5jvl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":903}' # _entry.id 5JVL # _exptl.entry_id 5JVL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 168.042 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description PHOSPHOENOLPYRUVATE _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 106.22 _cell.angle_beta 101.81 _cell.angle_gamma 98.32 _cell.entry_id 5JVL _cell.length_a 69.98 _cell.length_b 108.45 _cell.length_c 152.76 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,D,E,F,G,H,O,P,Q,R 1 1 B,C,I,J,K,L,M,N 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 ? 4 G N N ? 4 I N N ? 4 M N N ? 4 Q 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 OE1 GLU 324 A GLU 324 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc2 A OE1 GLN 336 A GLN 336 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc3 A OE1 GLU 748 A GLU 748 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc4 A OE2 GLU 748 A GLU 748 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc5 A OD2 ASP 772 A ASP 772 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc6 E O3G 6NQ . A 6NQ 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc7 E O2B 6NQ . A 6NQ 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.987 ? metalc ? metalc8 E O3A 6NQ . A 6NQ 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc9 G O2' PEP . A PEP 903 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc10 G O2 PEP . A PEP 903 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc11 G O3P PEP . A PEP 903 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc12 B OE1 GLU 748 B GLU 748 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc13 B OD2 ASP 772 B ASP 772 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc14 I O1 PEP . B PEP 901 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc15 I O2 PEP . B PEP 901 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc16 I O1P PEP . B PEP 901 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc17 C OE1 GLU 324 C GLU 324 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? metalc ? metalc18 C OE1 GLU 748 C GLU 748 1_555 N MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc19 C OD2 ASP 772 C ASP 772 1_555 N MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc20 K O3G 6NQ . C 6NQ 901 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc21 K O2B 6NQ . C 6NQ 901 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc22 K O3A 6NQ . C 6NQ 901 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc23 M O2' PEP . C PEP 903 1_555 N MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc24 M O2 PEP . C PEP 903 1_555 N MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc25 M O3P PEP . C PEP 903 1_555 N MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc26 D OE1 GLU 324 D GLU 324 1_555 P MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc27 D OE1 GLN 336 D GLN 336 1_555 P MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc28 D OE1 GLU 748 D GLU 748 1_555 R MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc29 D OD2 ASP 772 D ASP 772 1_555 R MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc30 O O2G 6NQ . D 6NQ 901 1_555 P MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc31 O O1B 6NQ . D 6NQ 901 1_555 P MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? metalc ? metalc32 O O3A 6NQ . D 6NQ 901 1_555 P MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc33 Q O1 PEP . D PEP 903 1_555 R MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc34 Q O2 PEP . D PEP 903 1_555 R MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc35 Q O1P PEP . D PEP 903 1_555 R MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? # _chem_comp.formula 'C3 H5 O6 P' _chem_comp.formula_weight 168.042 _chem_comp.id PEP _chem_comp.mon_nstd_flag . _chem_comp.name PHOSPHOENOLPYRUVATE _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 PEP doub 284 n n C1 O2' PEP sing 285 n n C1 C2 PEP sing 286 n n O2' HO2 PEP sing 287 n n C2 C3 PEP doub 288 n n C2 O2 PEP sing 289 n n C3 H31 PEP sing 290 n n C3 H32 PEP sing 291 n n O2 P PEP sing 292 n n P O1P PEP doub 293 n n P O2P PEP sing 294 n n P O3P PEP sing 295 n n O2P HOP2 PEP sing 296 n n O3P HOP3 PEP sing 297 n n # _atom_sites.entry_id 5JVL _atom_sites.fract_transf_matrix[1][1] 0.01429 _atom_sites.fract_transf_matrix[1][2] 0.002089 _atom_sites.fract_transf_matrix[1][3] 0.003855 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009319 _atom_sites.fract_transf_matrix[2][3] 0.003137 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007057 _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 6NQ A 1 901 875 6NQ DRG . F 3 MG A 1 902 876 MG MG . G 4 PEP A 1 903 877 PEP PEP . H 3 MG A 1 904 878 MG MG . I 4 PEP B 1 901 877 PEP PEP . J 3 MG B 1 902 878 MG MG . K 2 6NQ C 1 901 875 6NQ DRG . L 3 MG C 1 902 876 MG MG . M 4 PEP C 1 903 877 PEP PEP . N 3 MG C 1 904 878 MG MG . O 2 6NQ D 1 901 875 6NQ DRG . P 3 MG D 1 902 876 MG MG . Q 4 PEP D 1 903 877 PEP PEP . R 3 MG D 1 904 878 MG MG . # 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 PEP . . . M 4 21.655 -42.15 -128.612 1 26.13 ? C1 PEP 903 C 1 HETATM 2 O O1 PEP . . . M 4 22.238 -41.08 -128.892 1 25.06 ? O1 PEP 903 C 1 HETATM 3 O O2' PEP . . . M 4 21.688 -42.673 -127.468 1 26.82 ? O2' PEP 903 C 1 HETATM 4 C C2 PEP . . . M 4 20.922 -42.885 -129.626 1 25.49 ? C2 PEP 903 C 1 HETATM 5 C C3 PEP . . . M 4 21.126 -42.702 -130.926 1 24.41 ? C3 PEP 903 C 1 HETATM 6 O O2 PEP . . . M 4 19.994 -43.92 -129.164 1 26.97 ? O2 PEP 903 C 1 HETATM 7 P P PEP . . . M 4 18.687 -43.559 -128.302 1 31.45 ? P PEP 903 C 1 HETATM 8 O O1P PEP . . . M 4 17.496 -44.369 -128.804 1 27.55 ? O1P PEP 903 C 1 HETATM 9 O O2P PEP . . . M 4 18.276 -42.165 -128.749 1 34.93 ? O2P PEP 903 C 1 HETATM 10 O O3P PEP . . . M 4 19.309 -43.744 -126.882 1 25.65 ? O3P PEP 903 C 1 # _model_server_stats.io_time_ms 37 _model_server_stats.parse_time_ms 63 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 10 #