data_4L3V # _model_server_result.job_id KUe-ZmwNJHUNV0RIg2SU7Q _model_server_result.datetime_utc '2024-12-01 23:27:40' _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 4l3v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 4L3V # _exptl.entry_id 4L3V _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 3 _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 4L3V _cell.length_a 227.75 _cell.length_b 342.655 _cell.length_c 107.253 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L3V _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 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 1 1,2 B,C,F,G,H,I 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_353 -x-2,y,-z-3/2 -1 0 0 0 1 0 0 0 -1 -455.5 0 -160.8795 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 F 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 NZ LYS 118 B LYS 119 1_555 D C4A PLP . B PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 doub covale ? covale2 B NZ LYS 118 A LYS 119 1_555 F C4A PLP . A PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 doub covale ? covale3 C NZ LYS 118 C LYS 119 1_555 H C4A PLP . C PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.363 doub metalc ? metalc1 A SG CYS 51 B CYS 52 1_555 E FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc2 A NE2 HIS 64 B HIS 65 1_555 E FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc3 B SG CYS 51 A CYS 52 1_555 G FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc4 B NE2 HIS 64 A HIS 65 1_555 G FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc5 C SG CYS 51 C CYS 52 1_555 I FE HEM . C HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc6 C NE2 HIS 64 C HIS 65 1_555 I FE HEM . C HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? # _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 4L3V _atom_sites.fract_transf_matrix[1][1] 0.004391 _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] 0.002918 _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] 0.009324 _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 D 2 PLP B 1 601 1000 PLP PLP . E 3 HEM B 1 602 2000 HEM HEM . F 2 PLP A 1 601 1000 PLP PLP . G 3 HEM A 1 602 2000 HEM HEM . H 2 PLP C 1 601 1000 PLP PLP . I 3 HEM C 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 . . . D 2 -216.7 381.064 -90.609 1 30.94 ? N1 PLP 601 B 1 HETATM 2 C C2 PLP . . . D 2 -218.002 380.664 -90.81 1 33.29 ? C2 PLP 601 B 1 HETATM 3 C C2A PLP . . . D 2 -218.686 379.923 -89.716 1 19.55 ? C2A PLP 601 B 1 HETATM 4 C C3 PLP . . . D 2 -218.645 380.961 -92.011 1 32.55 ? C3 PLP 601 B 1 HETATM 5 O O3 PLP . . . D 2 -219.934 380.553 -92.228 1 42.26 ? O3 PLP 601 B 1 HETATM 6 C C4 PLP . . . D 2 -217.97 381.677 -93.004 1 30.45 ? C4 PLP 601 B 1 HETATM 7 C C4A PLP . . . D 2 -218.601 381.912 -94.331 1 33.68 ? C4A PLP 601 B 1 HETATM 8 C C5 PLP . . . D 2 -216.665 382.087 -92.78 1 29.35 ? C5 PLP 601 B 1 HETATM 9 C C6 PLP . . . D 2 -216.048 381.788 -91.577 1 34.54 ? C6 PLP 601 B 1 HETATM 10 C C5A PLP . . . D 2 -215.87 382.85 -93.797 1 32.65 ? C5A PLP 601 B 1 HETATM 11 O O4P PLP . . . D 2 -216.281 384.113 -94.174 1 43.38 ? O4P PLP 601 B 1 HETATM 12 P P PLP . . . D 2 -215.902 384.588 -95.658 1 40.05 ? P PLP 601 B 1 HETATM 13 O O1P PLP . . . D 2 -216.507 385.982 -95.823 1 25.32 ? O1P PLP 601 B 1 HETATM 14 O O2P PLP . . . D 2 -214.422 384.638 -95.81 1 33.79 -1 O2P PLP 601 B 1 HETATM 15 O O3P PLP . . . D 2 -216.532 383.588 -96.649 1 27.57 ? O3P PLP 601 B 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #