data_3O6D # _model_server_result.job_id yyvJi-tOG0vTJtP2modC5Q _model_server_result.datetime_utc '2024-12-15 03:10:11' _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 3o6d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 3O6D # _exptl.entry_id 3O6D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 249.158 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXINE-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 3O6D _cell.length_a 90.239 _cell.length_b 90.239 _cell.length_c 156.081 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3O6D _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 6_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 90.239 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 C ALA 3 A ALA 0 1_555 A N MSE 4 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C MSE 4 A MSE 1 1_555 A N LEU 5 A LEU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C ARG 20 A ARG 17 1_555 A N MSE 21 A MSE 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale4 A C MSE 21 A MSE 18 1_555 A N VAL 22 A VAL 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale5 A C GLU 253 A GLU 250 1_555 A N MSE 254 A MSE 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 A C MSE 254 A MSE 251 1_555 A N LYS 255 A LYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? # _chem_comp.formula 'C8 H12 N O6 P' _chem_comp.formula_weight 249.158 _chem_comp.id PXP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXINE-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PXP doub 281 n y N1 C6 PXP sing 282 n y C2 C2A PXP sing 283 n n C2 C3 PXP sing 284 n y C2A H2A1 PXP sing 285 n n C2A H2A2 PXP sing 286 n n C2A H2A3 PXP sing 287 n n C3 O3 PXP sing 288 n n C3 C4 PXP doub 289 n y O3 HO3 PXP sing 290 n n C4 C4A PXP sing 291 n n C4 C5 PXP sing 292 n y C4A O4A PXP sing 293 n n C4A H4A1 PXP sing 294 n n C4A H4A2 PXP sing 295 n n O4A HOA4 PXP sing 296 n n C5 C6 PXP doub 297 n y C5 C5A PXP sing 298 n n C6 H6 PXP sing 299 n n C5A O4P PXP sing 300 n n C5A H5A1 PXP sing 301 n n C5A H5A2 PXP sing 302 n n O4P P PXP sing 303 n n P O1P PXP doub 304 n n P O2P PXP sing 305 n n P O3P PXP sing 306 n n O2P HOP2 PXP sing 307 n n O3P HOP3 PXP sing 308 n n # _atom_sites.entry_id 3O6D _atom_sites.fract_transf_matrix[1][1] 0.011082 _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] 0.011082 _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] 0.006407 _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 B 2 PXP A 1 801 801 PXP PXP . C 3 PO4 A 1 802 802 PO4 PO4 . D 3 PO4 A 1 803 803 PO4 PO4 . E 4 HOH A 1 258 1 HOH HOH . E 4 HOH A 2 259 2 HOH HOH . E 4 HOH A 3 260 3 HOH HOH . E 4 HOH A 4 261 4 HOH HOH . E 4 HOH A 5 262 5 HOH HOH . E 4 HOH A 6 263 6 HOH HOH . E 4 HOH A 7 264 7 HOH HOH . E 4 HOH A 8 265 8 HOH HOH . E 4 HOH A 9 266 9 HOH HOH . E 4 HOH A 10 267 10 HOH HOH . E 4 HOH A 11 268 11 HOH HOH . E 4 HOH A 12 269 12 HOH HOH . E 4 HOH A 13 270 13 HOH HOH . E 4 HOH A 14 271 14 HOH HOH . E 4 HOH A 15 272 15 HOH HOH . E 4 HOH A 16 273 16 HOH HOH . E 4 HOH A 17 274 17 HOH HOH . E 4 HOH A 18 275 18 HOH HOH . E 4 HOH A 19 276 19 HOH HOH . E 4 HOH A 20 277 20 HOH HOH . E 4 HOH A 21 278 21 HOH HOH . E 4 HOH A 22 279 22 HOH HOH . E 4 HOH A 23 280 23 HOH HOH . E 4 HOH A 24 281 24 HOH HOH . E 4 HOH A 25 282 25 HOH HOH . E 4 HOH A 26 283 26 HOH HOH . E 4 HOH A 27 284 27 HOH HOH . E 4 HOH A 28 285 28 HOH HOH . E 4 HOH A 29 286 29 HOH HOH . E 4 HOH A 30 287 30 HOH HOH . E 4 HOH A 31 288 31 HOH HOH . E 4 HOH A 32 289 32 HOH HOH . E 4 HOH A 33 290 33 HOH HOH . E 4 HOH A 34 291 34 HOH HOH . E 4 HOH A 35 292 35 HOH HOH . E 4 HOH A 36 293 36 HOH HOH . E 4 HOH A 37 294 37 HOH HOH . E 4 HOH A 38 295 38 HOH HOH . E 4 HOH A 39 296 39 HOH HOH . E 4 HOH A 40 297 40 HOH HOH . E 4 HOH A 41 298 41 HOH HOH . E 4 HOH A 42 299 42 HOH HOH . E 4 HOH A 43 300 43 HOH HOH . E 4 HOH A 44 301 44 HOH HOH . E 4 HOH A 45 302 45 HOH HOH . E 4 HOH A 46 303 46 HOH HOH . E 4 HOH A 47 304 47 HOH HOH . E 4 HOH A 48 305 48 HOH HOH . E 4 HOH A 49 306 49 HOH HOH . E 4 HOH A 50 307 50 HOH HOH . E 4 HOH A 51 308 51 HOH HOH . E 4 HOH A 52 309 52 HOH HOH . E 4 HOH A 53 310 53 HOH HOH . E 4 HOH A 54 311 54 HOH HOH . E 4 HOH A 55 312 55 HOH HOH . E 4 HOH A 56 313 56 HOH HOH . E 4 HOH A 57 314 57 HOH HOH . E 4 HOH A 58 315 58 HOH HOH . E 4 HOH A 59 316 59 HOH HOH . E 4 HOH A 60 317 60 HOH HOH . E 4 HOH A 61 318 61 HOH HOH . E 4 HOH A 62 319 62 HOH HOH . E 4 HOH A 63 320 63 HOH HOH . E 4 HOH A 64 321 64 HOH HOH . E 4 HOH A 65 322 65 HOH HOH . E 4 HOH A 66 323 66 HOH HOH . E 4 HOH A 67 324 67 HOH HOH . E 4 HOH A 68 325 68 HOH HOH . E 4 HOH A 69 326 69 HOH HOH . E 4 HOH A 70 327 70 HOH HOH . E 4 HOH A 71 328 71 HOH HOH . E 4 HOH A 72 329 72 HOH HOH . E 4 HOH A 73 330 73 HOH HOH . E 4 HOH A 74 331 74 HOH HOH . E 4 HOH A 75 332 75 HOH HOH . E 4 HOH A 76 333 76 HOH HOH . E 4 HOH A 77 334 77 HOH HOH . E 4 HOH A 78 335 78 HOH HOH . E 4 HOH A 79 336 79 HOH HOH . E 4 HOH A 80 337 80 HOH HOH . E 4 HOH A 81 338 81 HOH HOH . E 4 HOH A 82 339 82 HOH HOH . E 4 HOH A 83 340 83 HOH HOH . E 4 HOH A 84 341 84 HOH HOH . E 4 HOH A 85 342 85 HOH HOH . E 4 HOH A 86 343 86 HOH HOH . E 4 HOH A 87 344 87 HOH HOH . E 4 HOH A 88 345 88 HOH HOH . E 4 HOH A 89 346 89 HOH HOH . E 4 HOH A 90 347 90 HOH HOH . E 4 HOH A 91 348 91 HOH HOH . E 4 HOH A 92 349 92 HOH HOH . E 4 HOH A 93 350 93 HOH HOH . E 4 HOH A 94 351 94 HOH HOH . E 4 HOH A 95 352 95 HOH HOH . E 4 HOH A 96 353 96 HOH HOH . E 4 HOH A 97 354 97 HOH HOH . E 4 HOH A 98 355 98 HOH HOH . E 4 HOH A 99 356 99 HOH HOH . E 4 HOH A 100 357 100 HOH HOH . E 4 HOH A 101 358 101 HOH HOH . E 4 HOH A 102 359 102 HOH HOH . E 4 HOH A 103 360 103 HOH HOH . E 4 HOH A 104 361 104 HOH HOH . E 4 HOH A 105 362 105 HOH HOH . E 4 HOH A 106 363 106 HOH HOH . E 4 HOH A 107 364 107 HOH HOH . E 4 HOH A 108 365 108 HOH HOH . E 4 HOH A 109 366 109 HOH HOH . E 4 HOH A 110 367 110 HOH HOH . E 4 HOH A 111 368 111 HOH HOH . E 4 HOH A 112 369 112 HOH HOH . E 4 HOH A 113 370 113 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 PXP . . . B 2 17.107 40.536 17.699 1 29.38 ? N1 PXP 801 A 1 HETATM 2 C C2 PXP . . . B 2 15.846 40.189 17.387 1 30.95 ? C2 PXP 801 A 1 HETATM 3 C C2A PXP . . . B 2 15.044 39.408 18.436 1 29.96 ? C2A PXP 801 A 1 HETATM 4 C C3 PXP . . . B 2 15.323 40.521 16.126 1 30.15 ? C3 PXP 801 A 1 HETATM 5 O O3 PXP . . . B 2 14.045 40.16 15.78 1 30.01 ? O3 PXP 801 A 1 HETATM 6 C C4 PXP . . . B 2 16.095 41.229 15.205 1 32.39 ? C4 PXP 801 A 1 HETATM 7 C C4A PXP . . . B 2 15.489 41.55 13.842 1 33.7 ? C4A PXP 801 A 1 HETATM 8 O O4A PXP . . . B 2 14.516 42.61 13.861 1 39.64 ? O4A PXP 801 A 1 HETATM 9 C C5 PXP . . . B 2 17.4 41.574 15.554 1 29.32 ? C5 PXP 801 A 1 HETATM 10 C C6 PXP . . . B 2 17.868 41.246 16.825 1 29.58 ? C6 PXP 801 A 1 HETATM 11 C C5A PXP . . . B 2 18.32 42.364 14.629 1 29.63 ? C5A PXP 801 A 1 HETATM 12 O O4P PXP . . . B 2 17.787 43.68 14.559 1 25.39 ? O4P PXP 801 A 1 HETATM 13 P P PXP . . . B 2 18.344 44.719 13.514 1 27.15 ? P PXP 801 A 1 HETATM 14 O O1P PXP . . . B 2 17.658 46.003 13.818 1 23.36 ? O1P PXP 801 A 1 HETATM 15 O O2P PXP . . . B 2 18.077 44.209 12.116 1 25.49 ? O2P PXP 801 A 1 HETATM 16 O O3P PXP . . . B 2 19.82 44.844 13.822 1 23.15 ? O3P PXP 801 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 16 #