data_8XHK # _model_server_result.job_id G3Wj3CuBTdMF2Y5d3WiRDQ _model_server_result.datetime_utc '2024-10-31 03:33:27' _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":"K","auth_seq_id":501}' # _entry.id 8XHK # _exptl.entry_id 8XHK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 233.158 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN 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 ? 3 J N N ? 3 K N N ? 3 L 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 H12 N O5 P' _chem_comp.formula_weight 233.158 _chem_comp.id PLR _chem_comp.mon_nstd_flag . _chem_comp.name '(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "4'-DEOXYPYRIDOXINE 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 PLR doub 286 n y N1 C6 PLR sing 287 n y C2 C2A PLR sing 288 n n C2 C3 PLR sing 289 n y C2A H2A1 PLR sing 290 n n C2A H2A2 PLR sing 291 n n C2A H2A3 PLR sing 292 n n C3 O3 PLR sing 293 n n C3 C4 PLR doub 294 n y O3 HO3 PLR sing 295 n n C4 C4A PLR sing 296 n n C4 C5 PLR sing 297 n y C4A H4A1 PLR sing 298 n n C4A H4A2 PLR sing 299 n n C4A H4A3 PLR sing 300 n n C5 C6 PLR doub 301 n y C5 C5A PLR sing 302 n n C6 H6 PLR sing 303 n n C5A O4P PLR sing 304 n n C5A H5A1 PLR sing 305 n n C5A H5A2 PLR sing 306 n n O4P P PLR sing 307 n n P O1P PLR doub 308 n n P O2P PLR sing 309 n n P O3P PLR sing 310 n n O2P H2P PLR sing 311 n n O3P H3P PLR sing 312 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 PLR . . . K 3 38.628 38.182 20.261 1 74.58 ? N1 PLR 501 E 1 HETATM 2 C C2 PLR . . . K 3 38.754 38.069 18.89 1 80.19 ? C2 PLR 501 E 1 HETATM 3 C C2A PLR . . . K 3 37.687 38.61 17.985 1 71.84 ? C2A PLR 501 E 1 HETATM 4 C C3 PLR . . . K 3 39.872 37.454 18.341 1 85.11 ? C3 PLR 501 E 1 HETATM 5 O O3 PLR . . . K 3 39.99 37.343 16.981 1 84.31 ? O3 PLR 501 E 1 HETATM 6 C C4 PLR . . . K 3 40.863 36.94 19.17 1 80.5 ? C4 PLR 501 E 1 HETATM 7 C C4A PLR . . . K 3 41.742 35.839 18.65 1 81.24 ? C4A PLR 501 E 1 HETATM 8 C C5 PLR . . . K 3 40.733 37.069 20.545 1 70.93 ? C5 PLR 501 E 1 HETATM 9 C C6 PLR . . . K 3 39.611 37.682 21.092 1 64.85 ? C6 PLR 501 E 1 HETATM 10 C C5A PLR . . . K 3 41.828 36.503 21.418 1 72.14 ? C5A PLR 501 E 1 HETATM 11 O O4P PLR . . . K 3 42.025 37.274 22.579 1 70.03 ? O4P PLR 501 E 1 HETATM 12 P P PLR . . . K 3 43.419 37.119 23.369 1 70.45 ? P PLR 501 E 1 HETATM 13 O O1P PLR . . . K 3 44.437 36.468 22.464 1 58.01 ? O1P PLR 501 E 1 HETATM 14 O O2P PLR . . . K 3 43.191 36.245 24.577 1 67.89 ? O2P PLR 501 E 1 HETATM 15 O O3P PLR . . . K 3 43.928 38.485 23.771 1 61.72 ? O3P PLR 501 E 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 15 #