data_2Q3D # _model_server_result.job_id mmDj2O6x74Qjdz3sHWIT_Q _model_server_result.datetime_utc '2024-10-10 13:24:25' _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 2q3d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":311}' # _entry.id 2Q3D # _exptl.entry_id 2Q3D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 320.236 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID' _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 2Q3D _cell.length_a 71.785 _cell.length_b 71.785 _cell.length_c 181.179 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Q3D _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 71.785 71.785 90.5895 # _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 # _chem_comp.formula 'C11 H17 N2 O7 P' _chem_comp.formula_weight 320.236 _chem_comp.id PDA _chem_comp.mon_nstd_flag . _chem_comp.name '2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms PYRIDOXYL-ALANINE-5-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 N C4A PDA sing 258 n n N CA PDA sing 259 n n N HN PDA sing 260 n n N1 C2 PDA doub 261 n y N1 C6 PDA sing 262 n y C2 C2A PDA sing 263 n n C2 C3 PDA sing 264 n y C2A H2A1 PDA sing 265 n n C2A H2A2 PDA sing 266 n n C2A H2A3 PDA sing 267 n n C3 O3A PDA sing 268 n n C3 C4 PDA doub 269 n y O3A HOA PDA sing 270 n n C4 C4A PDA sing 271 n n C4 C5 PDA sing 272 n y C4A H4A1 PDA sing 273 n n C4A H4A2 PDA sing 274 n n C5 C5A PDA sing 275 n n C5 C6 PDA doub 276 n y C5A OP4 PDA sing 277 n n C5A H5A1 PDA sing 278 n n C5A H5A2 PDA sing 279 n n OP4 P PDA sing 280 n n P OP1 PDA doub 281 n n P OP2 PDA sing 282 n n P OP3 PDA sing 283 n n OP2 HO2 PDA sing 284 n n OP3 HO3 PDA sing 285 n n C6 H6 PDA sing 286 n n CA CB PDA sing 287 n n CA C PDA sing 288 n n CA HA PDA sing 289 n n CB HB1 PDA sing 290 n n CB HB2 PDA sing 291 n n CB HB3 PDA sing 292 n n C O PDA sing 293 n n C OXT PDA doub 294 n n O HO PDA sing 295 n n # _atom_sites.entry_id 2Q3D _atom_sites.fract_transf_matrix[1][1] 0.01393 _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] 0.01393 _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] 0.005519 _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 PDA A 1 311 1 PDA PHA . C 3 MPD A 1 312 1 MPD MPD . D 4 HOH A 1 313 1 HOH HOH . D 4 HOH A 2 314 2 HOH HOH . D 4 HOH A 3 315 3 HOH HOH . D 4 HOH A 4 316 4 HOH HOH . D 4 HOH A 5 317 5 HOH HOH . D 4 HOH A 6 318 7 HOH HOH . D 4 HOH A 7 319 8 HOH HOH . D 4 HOH A 8 320 9 HOH HOH . D 4 HOH A 9 321 10 HOH HOH . D 4 HOH A 10 322 11 HOH HOH . D 4 HOH A 11 323 12 HOH HOH . D 4 HOH A 12 324 13 HOH HOH . D 4 HOH A 13 325 14 HOH HOH . D 4 HOH A 14 326 15 HOH HOH . D 4 HOH A 15 327 16 HOH HOH . D 4 HOH A 16 328 17 HOH HOH . D 4 HOH A 17 329 18 HOH HOH . D 4 HOH A 18 330 19 HOH HOH . D 4 HOH A 19 331 20 HOH HOH . D 4 HOH A 20 332 21 HOH HOH . D 4 HOH A 21 333 22 HOH HOH . D 4 HOH A 22 334 23 HOH HOH . D 4 HOH A 23 335 24 HOH HOH . D 4 HOH A 24 336 25 HOH HOH . D 4 HOH A 25 337 26 HOH HOH . D 4 HOH A 26 338 27 HOH HOH . D 4 HOH A 27 339 28 HOH HOH . D 4 HOH A 28 340 29 HOH HOH . D 4 HOH A 29 341 30 HOH HOH . D 4 HOH A 30 342 31 HOH HOH . D 4 HOH A 31 343 32 HOH HOH . D 4 HOH A 32 344 33 HOH HOH . D 4 HOH A 33 345 34 HOH HOH . D 4 HOH A 34 346 35 HOH HOH . D 4 HOH A 35 347 36 HOH HOH . D 4 HOH A 36 348 37 HOH HOH . D 4 HOH A 37 349 38 HOH HOH . D 4 HOH A 38 350 39 HOH HOH . D 4 HOH A 39 351 40 HOH HOH . D 4 HOH A 40 352 41 HOH HOH . D 4 HOH A 41 353 42 HOH HOH . D 4 HOH A 42 354 43 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 N PDA . . . B 2 35.743 13.889 43.116 1 48.22 ? N PDA 311 A 1 HETATM 2 N N1 PDA . . . B 2 37.169 14.451 47.899 1 39.64 ? N1 PDA 311 A 1 HETATM 3 C C2 PDA . . . B 2 37.151 15.287 46.846 1 39.97 ? C2 PDA 311 A 1 HETATM 4 C C2A PDA . . . B 2 37.616 16.731 47.048 1 41.5 ? C2A PDA 311 A 1 HETATM 5 C C3 PDA . . . B 2 36.732 14.825 45.586 1 41.84 ? C3 PDA 311 A 1 HETATM 6 O O3A PDA . . . B 2 36.738 15.649 44.508 1 40.68 ? O3A PDA 311 A 1 HETATM 7 C C4 PDA . . . B 2 36.322 13.487 45.435 1 40.26 ? C4 PDA 311 A 1 HETATM 8 C C4A PDA . . . B 2 35.836 12.894 44.162 1 42.15 ? C4A PDA 311 A 1 HETATM 9 C C5 PDA . . . B 2 36.347 12.657 46.557 1 40.53 ? C5 PDA 311 A 1 HETATM 10 C C5A PDA . . . B 2 35.946 11.171 46.454 1 42.1 ? C5A PDA 311 A 1 HETATM 11 O OP4 PDA . . . B 2 36.953 10.445 45.599 1 41.64 ? OP4 PDA 311 A 1 HETATM 12 P P PDA . . . B 2 36.505 9.027 44.857 1 41.94 ? P PDA 311 A 1 HETATM 13 O OP1 PDA . . . B 2 37.886 8.302 44.488 1 39.3 ? OP1 PDA 311 A 1 HETATM 14 O OP2 PDA . . . B 2 35.683 8.205 45.775 1 37.32 ? OP2 PDA 311 A 1 HETATM 15 O OP3 PDA . . . B 2 35.845 9.303 43.491 1 38.42 ? OP3 PDA 311 A 1 HETATM 16 C C6 PDA . . . B 2 36.779 13.172 47.779 1 40.26 ? C6 PDA 311 A 1 HETATM 17 C CA PDA . . . B 2 34.864 13.728 42.115 1 47.52 ? CA PDA 311 A 1 HETATM 18 C CB PDA . . . B 2 34.002 12.635 42.058 1 46.67 ? CB PDA 311 A 1 HETATM 19 C C PDA . . . B 2 34.844 14.789 41.039 1 47.16 ? C PDA 311 A 1 HETATM 20 O O PDA . . . B 2 34.029 14.652 40.101 1 47.43 ? O PDA 311 A 1 HETATM 21 O OXT PDA . . . B 2 35.647 15.752 41.163 1 46.02 ? OXT PDA 311 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #