data_8JG7 # _model_server_result.job_id wTOWzmHJqlcEoLl-AfB7OA _model_server_result.datetime_utc '2024-10-11 02:24:05' _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 8jg7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":501}' # _entry.id 8JG7 # _exptl.entry_id 8JG7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 109.18 _cell.angle_gamma 90 _cell.entry_id 8JG7 _cell.length_a 115.36 _cell.length_b 149.45 _cell.length_c 139.126 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JG7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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,N,O,P 1 1 B,C,H,I,J,K,L,M 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 E N N ? 2 H N N ? 2 K N N ? 2 N 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 E C4A PLP . A PLP 501 1_555 G C2 GOL . A GOL 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.591 ? covale ? covale2 H C4A PLP . C PLP 501 1_555 J C2 GOL . C GOL 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? covale ? covale3 K C4A PLP . D PLP 501 1_555 M C2 GOL . D GOL 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.597 ? covale ? covale4 N C4A PLP . E PLP 501 1_555 P C2 GOL . E GOL 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.577 ? metalc ? metalc1 A SG CYS 400 A CYS 466 1_555 F ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc2 A SG CYS 410 A CYS 476 1_555 F ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc3 A SG CYS 412 A CYS 478 1_555 F ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc4 A ND1 HIS 415 A HIS 481 1_555 F ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc5 B O CYS 400 C CYS 466 1_555 I ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc6 B SG CYS 400 C CYS 466 1_555 I ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc7 B SG CYS 410 C CYS 476 1_555 I ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc8 B SG CYS 412 C CYS 478 1_555 I ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc9 B ND1 HIS 415 C HIS 481 1_555 I ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc10 C SG CYS 400 D CYS 466 1_555 L ZN ZN . D ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc11 C SG CYS 410 D CYS 476 1_555 L ZN ZN . D ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc12 C SG CYS 412 D CYS 478 1_555 L ZN ZN . D ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc13 C ND1 HIS 415 D HIS 481 1_555 L ZN ZN . D ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc14 D O CYS 400 E CYS 466 1_555 O ZN ZN . E ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc15 D SG CYS 400 E CYS 466 1_555 O ZN ZN . E ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc16 D SG CYS 410 E CYS 476 1_555 O ZN ZN . E ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc17 D SG CYS 412 E CYS 478 1_555 O ZN ZN . E ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc18 D ND1 HIS 415 E HIS 481 1_555 O ZN ZN . E ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 N1 C2 PLP doub 271 n y N1 C6 PLP sing 272 n y C2 C2A PLP sing 273 n n C2 C3 PLP sing 274 n y C2A H2A1 PLP sing 275 n n C2A H2A2 PLP sing 276 n n C2A H2A3 PLP sing 277 n n C3 O3 PLP sing 278 n n C3 C4 PLP doub 279 n y O3 HO3 PLP sing 280 n n C4 C4A PLP sing 281 n n C4 C5 PLP sing 282 n y C4A O4A PLP doub 283 n n C4A H4A PLP sing 284 n n C5 C6 PLP doub 285 n y C5 C5A PLP sing 286 n n C6 H6 PLP sing 287 n n C5A O4P PLP sing 288 n n C5A H5A1 PLP sing 289 n n C5A H5A2 PLP sing 290 n n O4P P PLP sing 291 n n P O1P PLP doub 292 n n P O2P PLP sing 293 n n P O3P PLP sing 294 n n O2P HOP2 PLP sing 295 n n O3P HOP3 PLP sing 296 n n # _atom_sites.entry_id 8JG7 _atom_sites.fract_transf_matrix[1][1] 0.008669 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003015 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006691 _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] 0.00761 _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 PLP A 1 501 500 PLP PLP . F 3 ZN A 1 502 501 ZN ZN . G 4 GOL A 1 503 3 GOL GOL . H 2 PLP C 1 501 500 PLP PLP . I 3 ZN C 1 502 501 ZN ZN . J 4 GOL C 1 503 2 GOL GOL . K 2 PLP D 1 501 500 PLP PLP . L 3 ZN D 1 502 501 ZN ZN . M 4 GOL D 1 503 4 GOL GOL . N 2 PLP E 1 501 500 PLP PLP . O 3 ZN E 1 502 501 ZN ZN . P 4 GOL E 1 503 1 GOL GOL . # 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 N N1 PLP . . . N 2 130.283 63.972 39.523 1 53.52 ? N1 PLP 501 E 1 HETATM 2 C C2 PLP . . . N 2 130.316 63.663 40.822 1 47.59 ? C2 PLP 501 E 1 HETATM 3 C C2A PLP . . . N 2 129.305 64.261 41.738 1 45.56 ? C2A PLP 501 E 1 HETATM 4 C C3 PLP . . . N 2 131.3 62.796 41.324 1 50.59 ? C3 PLP 501 E 1 HETATM 5 O O3 PLP . . . N 2 131.271 62.535 42.682 1 53.71 ? O3 PLP 501 E 1 HETATM 6 C C4 PLP . . . N 2 132.247 62.215 40.439 1 47.09 ? C4 PLP 501 E 1 HETATM 7 C C4A PLP . . . N 2 133.297 61.348 41.01 1 51.74 ? C4A PLP 501 E 1 HETATM 8 C C5 PLP . . . N 2 132.177 62.559 39.06 1 49.42 ? C5 PLP 501 E 1 HETATM 9 C C6 PLP . . . N 2 131.192 63.433 38.665 1 52.52 ? C6 PLP 501 E 1 HETATM 10 C C5A PLP . . . N 2 133.16 62.079 38.021 1 47.08 ? C5A PLP 501 E 1 HETATM 11 O O4P PLP . . . N 2 132.766 60.846 37.342 1 45.12 ? O4P PLP 501 E 1 HETATM 12 P P PLP . . . N 2 133.862 59.719 36.85 1 54.31 ? P PLP 501 E 1 HETATM 13 O O1P PLP . . . N 2 134.405 60.234 35.509 1 53.76 ? O1P PLP 501 E 1 HETATM 14 O O2P PLP . . . N 2 133.038 58.451 36.689 1 45.25 ? O2P PLP 501 E 1 HETATM 15 O O3P PLP . . . N 2 134.975 59.57 37.904 1 45.94 ? O3P PLP 501 E 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 15 #