data_5ZSK # _model_server_result.job_id QLNfsMhKSFYK70LKM3hA9g _model_server_result.datetime_utc '2024-11-28 16:12:04' _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 5zsk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5ZSK # _exptl.entry_id 5ZSK _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 120 _cell.entry_id 5ZSK _cell.length_a 91.8 _cell.length_b 91.8 _cell.length_c 127.5 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZSK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -85 # _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 HIS 363 A HIS 360 1_555 A N CSS 364 A CSS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C CSS 364 A CSS 361 1_555 A N ALA 365 A ALA 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _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 5ZSK _atom_sites.fract_transf_matrix[1][1] 0.010893 _atom_sites.fract_transf_matrix[1][2] 0.006289 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012578 _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] 0.007843 _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 1 501 1 PDA PDA . C 3 HOH A 1 601 2 HOH HOH . C 3 HOH A 2 602 6 HOH HOH . C 3 HOH A 3 603 5 HOH HOH . C 3 HOH A 4 604 9 HOH HOH . C 3 HOH A 5 605 3 HOH HOH . C 3 HOH A 6 606 4 HOH HOH . C 3 HOH A 7 607 1 HOH HOH . C 3 HOH A 8 608 8 HOH HOH . C 3 HOH A 9 609 7 HOH HOH . C 3 HOH A 10 610 11 HOH HOH . C 3 HOH A 11 611 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 N PDA . . . B 2 -36.891 32.739 -37.194 1 68.11 ? N PDA 501 A 1 HETATM 2 N N1 PDA . . . B 2 -33.288 31.008 -34.235 1 58.62 ? N1 PDA 501 A 1 HETATM 3 C C2 PDA . . . B 2 -34.591 31.25 -33.975 1 51.07 ? C2 PDA 501 A 1 HETATM 4 C C2A PDA . . . B 2 -35.225 30.706 -32.702 1 39.28 ? C2A PDA 501 A 1 HETATM 5 C C3 PDA . . . B 2 -35.35 31.993 -34.859 1 58.69 ? C3 PDA 501 A 1 HETATM 6 O O3A PDA . . . B 2 -36.697 32.232 -34.57 1 57.48 ? O3A PDA 501 A 1 HETATM 7 C C4 PDA . . . B 2 -34.775 32.471 -35.993 1 60.3 ? C4 PDA 501 A 1 HETATM 8 C C4A PDA . . . B 2 -35.568 33.294 -37.002 1 64.46 ? C4A PDA 501 A 1 HETATM 9 C C5 PDA . . . B 2 -33.469 32.227 -36.245 1 53.79 ? C5 PDA 501 A 1 HETATM 10 C C5A PDA . . . B 2 -32.839 32.763 -37.519 1 47.54 ? C5A PDA 501 A 1 HETATM 11 O OP4 PDA . . . B 2 -31.722 33.538 -37.216 1 41.58 ? OP4 PDA 501 A 1 HETATM 12 P P PDA . . . B 2 -31.551 34.842 -38.198 1 48.31 ? P PDA 501 A 1 HETATM 13 O OP1 PDA . . . B 2 -32.592 34.71 -39.285 1 60.22 ? OP1 PDA 501 A 1 HETATM 14 O OP2 PDA . . . B 2 -31.82 36.108 -37.411 1 48.32 ? OP2 PDA 501 A 1 HETATM 15 O OP3 PDA . . . B 2 -30.165 34.869 -38.82 1 53.43 ? OP3 PDA 501 A 1 HETATM 16 C C6 PDA . . . B 2 -32.714 31.485 -35.36 1 55.4 ? C6 PDA 501 A 1 HETATM 17 C CA PDA . . . B 2 -37.441 33.261 -38.434 1 62.11 ? CA PDA 501 A 1 HETATM 18 C CB PDA . . . B 2 -36.708 32.673 -39.644 1 48.31 ? CB PDA 501 A 1 HETATM 19 C C PDA . . . B 2 -38.931 32.927 -38.478 1 69.5 ? C PDA 501 A 1 HETATM 20 O O PDA . . . B 2 -39.641 33.119 -37.454 1 64.83 ? O PDA 501 A 1 HETATM 21 O OXT PDA . . . B 2 -39.444 32.449 -39.528 1 73.19 ? OXT PDA 501 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #