data_4L0D # _model_server_result.job_id dS3E7dQTufP7WqfQD9sI0g _model_server_result.datetime_utc '2024-11-29 16:30:35' _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 4l0d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 4L0D # _exptl.entry_id 4L0D _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 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 4L0D _cell.length_a 124.365 _cell.length_b 136.203 _cell.length_c 169.307 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L0D _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 E 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 NZ LYS 119 A LYS 119 1_555 C C4A PLP . A PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 doub covale ? covale2 B NZ LYS 119 B LYS 119 1_555 E C4A PLP . B PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 doub metalc ? metalc1 A SG CYS 52 A CYS 52 1_555 D FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc2 A NE2 HIS 65 A HIS 65 1_555 D FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc3 B SG CYS 52 B CYS 52 1_555 F FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc4 B NE2 HIS 65 B HIS 65 1_555 F FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? # _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 340 n y N1 C6 PLP sing 341 n y C2 C2A PLP sing 342 n n C2 C3 PLP sing 343 n y C2A H2A1 PLP sing 344 n n C2A H2A2 PLP sing 345 n n C2A H2A3 PLP sing 346 n n C3 O3 PLP sing 347 n n C3 C4 PLP doub 348 n y O3 HO3 PLP sing 349 n n C4 C4A PLP sing 350 n n C4 C5 PLP sing 351 n y C4A O4A PLP doub 352 n n C4A H4A PLP sing 353 n n C5 C6 PLP doub 354 n y C5 C5A PLP sing 355 n n C6 H6 PLP sing 356 n n C5A O4P PLP sing 357 n n C5A H5A1 PLP sing 358 n n C5A H5A2 PLP sing 359 n n O4P P PLP sing 360 n n P O1P PLP doub 361 n n P O2P PLP sing 362 n n P O3P PLP sing 363 n n O2P HOP2 PLP sing 364 n n O3P HOP3 PLP sing 365 n n # _atom_sites.entry_id 4L0D _atom_sites.fract_transf_matrix[1][1] 0.008041 _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] 0.007342 _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] 0.005906 _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 C 2 PLP A 1 601 1000 PLP PLP . D 3 HEM A 1 602 2000 HEM HEM . E 2 PLP B 1 601 1000 PLP PLP . F 3 HEM B 1 602 2000 HEM HEM . # 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 . . . C 2 -19.68 -18.707 -25.387 1 73.76 ? N1 PLP 601 A 1 HETATM 2 C C2 PLP . . . C 2 -19.222 -19.964 -25.723 1 66.86 ? C2 PLP 601 A 1 HETATM 3 C C2A PLP . . . C 2 -19.674 -20.612 -26.997 1 58.71 ? C2A PLP 601 A 1 HETATM 4 C C3 PLP . . . C 2 -18.346 -20.635 -24.876 1 69.99 ? C3 PLP 601 A 1 HETATM 5 O O3 PLP . . . C 2 -17.896 -21.886 -25.207 1 69.49 ? O3 PLP 601 A 1 HETATM 6 C C4 PLP . . . C 2 -17.933 -20.04 -23.696 1 86.22 ? C4 PLP 601 A 1 HETATM 7 C C4A PLP . . . C 2 -17.259 -20.881 -22.663 1 79.04 ? C4A PLP 601 A 1 HETATM 8 C C5 PLP . . . C 2 -18.395 -18.773 -23.367 1 75.42 ? C5 PLP 601 A 1 HETATM 9 C C6 PLP . . . C 2 -19.263 -18.116 -24.215 1 75.5 ? C6 PLP 601 A 1 HETATM 10 C C5A PLP . . . C 2 -18.002 -18.075 -22.092 1 81.87 ? C5A PLP 601 A 1 HETATM 11 O O4P PLP . . . C 2 -16.623 -17.843 -21.935 1 83.28 ? O4P PLP 601 A 1 HETATM 12 P P PLP . . . C 2 -16.084 -17.74 -20.409 1 82.93 ? P PLP 601 A 1 HETATM 13 O O1P PLP . . . C 2 -14.614 -17.4 -20.424 1 80.98 ? O1P PLP 601 A 1 HETATM 14 O O2P PLP . . . C 2 -16.867 -16.684 -19.639 1 85.5 1 O2P PLP 601 A 1 HETATM 15 O O3P PLP . . . C 2 -16.247 -19.098 -19.758 1 77.83 ? O3P PLP 601 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #