data_5XT6 # _model_server_result.job_id LE5j_i5OkSX4FU0BVsy8zA _model_server_result.datetime_utc '2024-10-10 15:23:11' _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 5xt6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 5XT6 # _exptl.entry_id 5XT6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 320.236 _entity.id 5 _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 2 _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 120 _cell.entry_id 5XT6 _cell.length_a 73.93 _cell.length_b 73.93 _cell.length_c 367.74 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XT6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 5 F N N ? 5 G 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 B C HIS 363 A HIS 360 1_555 B N CSS 364 A CSS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale2 B C CSS 364 A CSS 361 1_555 B N ALA 365 A ALA 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale3 C C HIS 363 B HIS 360 1_555 C N CSS 364 B CSS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale4 C C CSS 364 B CSS 361 1_555 C N ALA 365 B ALA 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 D C THR 40 C THR 40 1_555 D N CSS 41 C CSS 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale6 D C CSS 41 C CSS 41 1_555 D N GLY 42 C GLY 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? metalc ? metalc1 A OD2 ASP 43 D ASP 43 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc2 A SG CYS 66 D CYS 66 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc3 A SG CYS 128 D CYS 128 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc4 E ZN ZN . D ZN 201 1_555 C ND1 HIS 345 B HIS 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc5 B ND1 HIS 345 A HIS 342 1_555 H ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc6 D OD1 ASP 43 C ASP 43 1_555 H ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc7 D OD2 ASP 43 C ASP 43 1_555 H ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc8 D SG CYS 66 C CYS 66 1_555 H ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc9 D SG CYS 128 C CYS 128 1_555 H ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? # _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 251 n n N CA PDA sing 252 n n N HN PDA sing 253 n n N1 C2 PDA doub 254 n y N1 C6 PDA sing 255 n y C2 C2A PDA sing 256 n n C2 C3 PDA sing 257 n y C2A H2A1 PDA sing 258 n n C2A H2A2 PDA sing 259 n n C2A H2A3 PDA sing 260 n n C3 O3A PDA sing 261 n n C3 C4 PDA doub 262 n y O3A HOA PDA sing 263 n n C4 C4A PDA sing 264 n n C4 C5 PDA sing 265 n y C4A H4A1 PDA sing 266 n n C4A H4A2 PDA sing 267 n n C5 C5A PDA sing 268 n n C5 C6 PDA doub 269 n y C5A OP4 PDA sing 270 n n C5A H5A1 PDA sing 271 n n C5A H5A2 PDA sing 272 n n OP4 P PDA sing 273 n n P OP1 PDA doub 274 n n P OP2 PDA sing 275 n n P OP3 PDA sing 276 n n OP2 HO2 PDA sing 277 n n OP3 HO3 PDA sing 278 n n C6 H6 PDA sing 279 n n CA CB PDA sing 280 n n CA C PDA sing 281 n n CA HA PDA sing 282 n n CB HB1 PDA sing 283 n n CB HB2 PDA sing 284 n n CB HB3 PDA sing 285 n n C O PDA sing 286 n n C OXT PDA doub 287 n n O HO PDA sing 288 n n # _atom_sites.entry_id 5XT6 _atom_sites.fract_transf_matrix[1][1] 0.013526 _atom_sites.fract_transf_matrix[1][2] 0.007809 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015619 _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] 0.002719 _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 E 4 ZN D 1 201 150 ZN ZN . F 5 PDA A 1 501 1 PDA PDA . G 5 PDA B 1 501 2 PDA PDA . H 4 ZN C 1 201 150 ZN ZN . I 6 HOH A 1 601 2 HOH HOH . I 6 HOH A 2 602 3 HOH HOH . I 6 HOH A 3 603 1 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 . . . F 5 8.899 3.832 -9.895 1 94.9 ? N PDA 501 A 1 HETATM 2 N N1 PDA . . . F 5 9.318 7.748 -12.865 1 97.76 ? N1 PDA 501 A 1 HETATM 3 C C2 PDA . . . F 5 10.225 6.763 -12.652 1 94.96 ? C2 PDA 501 A 1 HETATM 4 C C2A PDA . . . F 5 11.417 6.678 -13.573 1 88.81 ? C2A PDA 501 A 1 HETATM 5 C C3 PDA . . . F 5 10.02 5.804 -11.524 1 96.74 ? C3 PDA 501 A 1 HETATM 6 O O3A PDA . . . F 5 10.928 4.815 -11.296 1 97.24 ? O3A PDA 501 A 1 HETATM 7 C C4 PDA . . . F 5 8.797 5.999 -10.682 1 97.09 ? C4 PDA 501 A 1 HETATM 8 C C4A PDA . . . F 5 8.467 5.131 -9.514 1 94.67 ? C4A PDA 501 A 1 HETATM 9 C C5 PDA . . . F 5 7.885 7.117 -11.029 1 102.27 ? C5 PDA 501 A 1 HETATM 10 C C5A PDA . . . F 5 6.629 7.374 -10.213 1 107.86 ? C5A PDA 501 A 1 HETATM 11 O OP4 PDA . . . F 5 6.987 7.627 -8.84 1 96.7 ? OP4 PDA 501 A 1 HETATM 12 P P PDA . . . F 5 6.005 7.306 -7.613 1 81.74 ? P PDA 501 A 1 HETATM 13 O OP1 PDA . . . F 5 5.385 5.974 -7.97 1 83.71 ? OP1 PDA 501 A 1 HETATM 14 O OP2 PDA . . . F 5 5.038 8.47 -7.564 1 82.98 ? OP2 PDA 501 A 1 HETATM 15 O OP3 PDA . . . F 5 7.002 7.278 -6.491 1 81.9 ? OP3 PDA 501 A 1 HETATM 16 C C6 PDA . . . F 5 8.209 7.936 -12.12 1 100.46 ? C6 PDA 501 A 1 HETATM 17 C CA PDA . . . F 5 8.156 2.594 -9.916 1 94.37 ? CA PDA 501 A 1 HETATM 18 C CB PDA . . . F 5 6.651 2.761 -10.197 1 76 ? CB PDA 501 A 1 HETATM 19 C C PDA . . . F 5 8.922 1.686 -10.864 1 104.1 ? C PDA 501 A 1 HETATM 20 O O PDA . . . F 5 9.726 0.825 -10.423 1 101.09 ? O PDA 501 A 1 HETATM 21 O OXT PDA . . . F 5 8.796 1.849 -12.095 1 127.5 ? OXT PDA 501 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #