data_5WT6 # _model_server_result.job_id 5-4Jd4vGxKnr8wQtg2_mMA _model_server_result.datetime_utc '2024-11-27 17:02:53' _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 5wt6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 5WT6 # _exptl.entry_id 5WT6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 320.236 _entity.id 4 _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 5WT6 _cell.length_a 102.75 _cell.length_b 102.75 _cell.length_c 131.97 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WT6 _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 _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 327 A ALA 327 1_555 A N CSS 328 A CSS 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C CSS 328 A CSS 328 1_555 A N ALA 329 A ALA 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? # _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 262 n n N CA PDA sing 263 n n N HN PDA sing 264 n n N1 C2 PDA doub 265 n y N1 C6 PDA sing 266 n y C2 C2A PDA sing 267 n n C2 C3 PDA sing 268 n y C2A H2A1 PDA sing 269 n n C2A H2A2 PDA sing 270 n n C2A H2A3 PDA sing 271 n n C3 O3A PDA sing 272 n n C3 C4 PDA doub 273 n y O3A HOA PDA sing 274 n n C4 C4A PDA sing 275 n n C4 C5 PDA sing 276 n y C4A H4A1 PDA sing 277 n n C4A H4A2 PDA sing 278 n n C5 C5A PDA sing 279 n n C5 C6 PDA doub 280 n y C5A OP4 PDA sing 281 n n C5A H5A1 PDA sing 282 n n C5A H5A2 PDA sing 283 n n OP4 P PDA sing 284 n n P OP1 PDA doub 285 n n P OP2 PDA sing 286 n n P OP3 PDA sing 287 n n OP2 HO2 PDA sing 288 n n OP3 HO3 PDA sing 289 n n C6 H6 PDA sing 290 n n CA CB PDA sing 291 n n CA C PDA sing 292 n n CA HA PDA sing 293 n n CB HB1 PDA sing 294 n n CB HB2 PDA sing 295 n n CB HB3 PDA sing 296 n n C O PDA sing 297 n n C OXT PDA doub 298 n n O HO PDA sing 299 n n # _atom_sites.entry_id 5WT6 _atom_sites.fract_transf_matrix[1][1] 0.009732 _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] 0.009732 _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] 0.007577 _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 IPA A 1 501 1 IPA IPA . C 3 CL A 1 502 1 CL CL . D 4 PDA A 1 503 1 PDA PDA . E 5 HOH A 1 601 13 HOH HOH . E 5 HOH A 2 602 2 HOH HOH . E 5 HOH A 3 603 10 HOH HOH . E 5 HOH A 4 604 4 HOH HOH . E 5 HOH A 5 605 11 HOH HOH . E 5 HOH A 6 606 7 HOH HOH . E 5 HOH A 7 607 12 HOH HOH . E 5 HOH A 8 608 6 HOH HOH . E 5 HOH A 9 609 8 HOH HOH . E 5 HOH A 10 610 5 HOH HOH . E 5 HOH A 11 611 1 HOH HOH . E 5 HOH A 12 612 9 HOH HOH . E 5 HOH A 13 613 3 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 . . . D 4 -23.248 -18.381 -15.796 1 86.29 ? N PDA 503 A 1 HETATM 2 N N1 PDA . . . D 4 -18.401 -18.848 -14.536 1 80.17 ? N1 PDA 503 A 1 HETATM 3 C C2 PDA . . . D 4 -19.112 -19.073 -15.68 1 80.56 ? C2 PDA 503 A 1 HETATM 4 C C2A PDA . . . D 4 -18.368 -19.384 -16.983 1 80.81 ? C2A PDA 503 A 1 HETATM 5 C C3 PDA . . . D 4 -20.504 -19.02 -15.662 1 80.24 ? C3 PDA 503 A 1 HETATM 6 O O3A PDA . . . D 4 -21.277 -19.258 -16.889 1 79.72 ? O3A PDA 503 A 1 HETATM 7 C C4 PDA . . . D 4 -21.164 -18.737 -14.481 1 80.62 ? C4 PDA 503 A 1 HETATM 8 C C4A PDA . . . D 4 -22.708 -18.658 -14.42 1 83.24 ? C4A PDA 503 A 1 HETATM 9 C C5 PDA . . . D 4 -20.444 -18.509 -13.346 1 77.67 ? C5 PDA 503 A 1 HETATM 10 C C5A PDA . . . D 4 -21.201 -18.2 -12.037 1 72.71 ? C5A PDA 503 A 1 HETATM 11 O OP4 PDA . . . D 4 -21.242 -19.422 -11.266 1 68.21 ? OP4 PDA 503 A 1 HETATM 12 P P PDA . . . D 4 -21.779 -19.277 -9.684 1 65.18 ? P PDA 503 A 1 HETATM 13 O OP1 PDA . . . D 4 -23.112 -18.539 -9.709 1 65.99 ? OP1 PDA 503 A 1 HETATM 14 O OP2 PDA . . . D 4 -20.765 -18.447 -8.882 1 65.52 ? OP2 PDA 503 A 1 HETATM 15 O OP3 PDA . . . D 4 -21.94 -20.689 -9.044 1 64.78 ? OP3 PDA 503 A 1 HETATM 16 C C6 PDA . . . D 4 -19.065 -18.565 -13.357 1 79.17 ? C6 PDA 503 A 1 HETATM 17 C CA PDA . . . D 4 -24.697 -18.028 -15.753 1 85.28 ? CA PDA 503 A 1 HETATM 18 C CB PDA . . . D 4 -24.984 -17.015 -14.643 1 84.99 ? CB PDA 503 A 1 HETATM 19 C C PDA . . . D 4 -25.095 -17.472 -17.101 1 83.99 ? C PDA 503 A 1 HETATM 20 O O PDA . . . D 4 -26.277 -17.194 -17.345 1 83.41 ? O PDA 503 A 1 HETATM 21 O OXT PDA . . . D 4 -24.244 -17.302 -17.947 1 83.37 ? OXT PDA 503 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 21 #