data_8XHK # _model_server_result.job_id 3Dwr9YDnOOjgzJfBchHylQ _model_server_result.datetime_utc '2024-11-25 15:18:01' _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 8xhk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 8XHK # _exptl.entry_id 8XHK _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 8XHK _cell.length_a 65.11 _cell.length_b 110.59 _cell.length_c 354.667 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XHK _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab (z,x,y)' _symmetry.space_group_name_H-M 'P 2 21 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 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,M,N 1 1 C,E,I,K,O,Q 2 1 D,F,J,L,P,R 3 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 G N N ? 2 H N N ? 2 I 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 244 C LYS 254 1_555 G C4A PLP . C PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 B NZ LYS 244 A LYS 254 1_555 H C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale3 C NZ LYS 244 B LYS 254 1_555 I C4A PLP . B PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? # _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 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 8XHK _atom_sites.fract_transf_matrix[1][1] 0.015359 _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] 0.009042 _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] 0.00282 _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 G 2 PLP C 1 501 501 PLP PLP . H 2 PLP A 1 501 501 PLP PLP . I 2 PLP B 1 501 501 PLP PLP . J 3 PLR D 1 501 501 PLR PLP . K 3 PLR E 1 501 501 PLR PLP . L 3 PLR F 1 501 501 PLR PLP . M 4 HOH C 1 601 12 HOH HOH . N 4 HOH A 1 601 6 HOH HOH . N 4 HOH A 2 602 17 HOH HOH . N 4 HOH A 3 603 7 HOH HOH . N 4 HOH A 4 604 8 HOH HOH . N 4 HOH A 5 605 11 HOH HOH . N 4 HOH A 6 606 9 HOH HOH . O 4 HOH B 1 601 15 HOH HOH . O 4 HOH B 2 602 1 HOH HOH . O 4 HOH B 3 603 14 HOH HOH . O 4 HOH B 4 604 3 HOH HOH . O 4 HOH B 5 605 13 HOH HOH . P 4 HOH D 1 601 2 HOH HOH . P 4 HOH D 2 602 16 HOH HOH . Q 4 HOH E 1 601 18 HOH HOH . R 4 HOH F 1 601 4 HOH HOH . R 4 HOH F 2 602 5 HOH HOH . R 4 HOH F 3 603 10 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 N N1 PLP . . . I 2 45.942 27.148 40.139 1 53.2 ? N1 PLP 501 B 1 HETATM 2 C C2 PLP . . . I 2 46.422 27.156 41.436 1 57.92 ? C2 PLP 501 B 1 HETATM 3 C C2A PLP . . . I 2 46.348 25.916 42.278 1 51.43 ? C2A PLP 501 B 1 HETATM 4 C C3 PLP . . . I 2 46.978 28.313 41.965 1 60.21 ? C3 PLP 501 B 1 HETATM 5 O O3 PLP . . . I 2 47.455 28.325 43.248 1 81.26 ? O3 PLP 501 B 1 HETATM 6 C C4 PLP . . . I 2 47.049 29.464 41.193 1 72.92 ? C4 PLP 501 B 1 HETATM 7 C C4A PLP . . . I 2 47.8 30.664 41.687 1 75.87 ? C4A PLP 501 B 1 HETATM 8 C C5 PLP . . . I 2 46.57 29.452 39.892 1 74.3 ? C5 PLP 501 B 1 HETATM 9 C C6 PLP . . . I 2 46.01 28.292 39.365 1 55.9 ? C6 PLP 501 B 1 HETATM 10 C C5A PLP . . . I 2 46.665 30.725 39.087 1 72.99 ? C5A PLP 501 B 1 HETATM 11 O O4P PLP . . . I 2 46.856 30.447 37.721 1 68.5 ? O4P PLP 501 B 1 HETATM 12 P P PLP . . . I 2 47.266 31.653 36.74 1 63.28 ? P PLP 501 B 1 HETATM 13 O O1P PLP . . . I 2 46.242 31.753 35.636 1 55.2 ? O1P PLP 501 B 1 HETATM 14 O O2P PLP . . . I 2 48.646 31.387 36.184 1 59.23 ? O2P PLP 501 B 1 HETATM 15 O O3P PLP . . . I 2 47.292 32.944 37.522 1 53.16 ? O3P PLP 501 B 1 # _model_server_stats.io_time_ms 121 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 15 #