data_1PYG # _model_server_result.job_id F4MBzLX5H1bXxoV3U0zU0A _model_server_result.datetime_utc '2025-02-05 11:52:25' _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 1pyg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":860}' # _entry.id 1PYG # _exptl.entry_id 1PYG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 327.122 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 1PYG _cell.length_a 169.9 _cell.length_b 209.9 _cell.length_c 123.4 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PYG _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PQS _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,J,K,L _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 ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L 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 A NZ LYS 680 A LYS 680 1_555 F C4A PDP . A PDP 860 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.594 ? covale ? covale2 A NZ LYS 680 A LYS 680 1_555 F C4A PDP . A PDP 860 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.439 ? covale ? covale3 B NZ LYS 680 B LYS 680 1_555 H C4A PDP . B PDP 860 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.458 ? covale ? covale4 B NZ LYS 680 B LYS 680 1_555 H C4A PDP . B PDP 860 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.449 ? covale ? covale5 C NZ LYS 680 C LYS 680 1_555 J C4A PDP . C PDP 860 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.428 ? covale ? covale6 C NZ LYS 680 C LYS 680 1_555 J C4A PDP . C PDP 860 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.563 ? covale ? covale7 D NZ LYS 680 D LYS 680 1_555 L C4A PDP . D PDP 860 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.347 ? covale ? covale8 D NZ LYS 680 D LYS 680 1_555 L C4A PDP . D PDP 860 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.445 ? # _chem_comp.formula 'C8 H11 N O9 P2' _chem_comp.formula_weight 327.122 _chem_comp.id PDP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-DIPHOSPHATE" _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 PDP doub 274 n y N1 C6 PDP sing 275 n y C2 C2A PDP sing 276 n n C2 C3 PDP sing 277 n y C2A H2A1 PDP sing 278 n n C2A H2A2 PDP sing 279 n n C2A H2A3 PDP sing 280 n n C3 O3 PDP sing 281 n n C3 C4 PDP doub 282 n y O3 HO3 PDP sing 283 n n C4 C4A PDP sing 284 n n C4 C5 PDP sing 285 n y C4A O4A PDP doub 286 n n C4A H4A PDP sing 287 n n C5 C6 PDP doub 288 n y C5 C5A PDP sing 289 n n C6 H6 PDP sing 290 n n C5A O5A PDP sing 291 n n C5A H5A1 PDP sing 292 n n C5A H5A2 PDP sing 293 n n O5A PA PDP sing 294 n n PA O1A PDP doub 295 n n PA O3A PDP sing 296 n n PA O2A PDP sing 297 n n O3A PB PDP sing 298 n n O2A HOA2 PDP sing 299 n n PB O1B PDP doub 300 n n PB O2B PDP sing 301 n n PB O3B PDP sing 302 n n O2B HOB2 PDP sing 303 n n O3B HOB3 PDP sing 304 n n # _atom_sites.entry_id 1PYG _atom_sites.fract_transf_matrix[1][1] 0.005886 _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] 0.004764 _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] 0.008104 _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 2 AMP A 1 843 841 AMP AMP . F 3 PDP A 1 860 860 PDP PDP . G 2 AMP B 1 843 841 AMP AMP . H 3 PDP B 1 860 860 PDP PDP . I 2 AMP C 1 843 841 AMP AMP . J 3 PDP C 1 860 860 PDP PDP . K 2 AMP D 1 843 841 AMP AMP . L 3 PDP D 1 860 860 PDP PDP . # 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 PDP . A . H 3 71.295 42.321 7.668 0.5 52.41 ? N1 PDP 860 B 1 HETATM 2 N N1 PDP . B . H 3 71.309 42.288 7.668 0.5 51.13 ? N1 PDP 860 B 1 HETATM 3 C C2 PDP . A . H 3 71.513 40.986 7.78 0.5 52.29 ? C2 PDP 860 B 1 HETATM 4 C C2 PDP . B . H 3 71.573 40.964 7.782 0.5 51.26 ? C2 PDP 860 B 1 HETATM 5 C C2A PDP . A . H 3 70.593 40.165 8.642 0.5 50.55 ? C2A PDP 860 B 1 HETATM 6 C C2A PDP . B . H 3 70.663 40.111 8.618 0.5 49.46 ? C2A PDP 860 B 1 HETATM 7 C C3 PDP . A . H 3 72.534 40.396 7.087 0.5 52.89 ? C3 PDP 860 B 1 HETATM 8 C C3 PDP . B . H 3 72.617 40.393 7.095 0.5 51.48 ? C3 PDP 860 B 1 HETATM 9 O O3 PDP . A . H 3 72.734 39.043 7.189 0.5 53.9 ? O3 PDP 860 B 1 HETATM 10 O O3 PDP . B . H 3 72.797 39.034 7.154 0.5 52.15 ? O3 PDP 860 B 1 HETATM 11 C C4 PDP . A . H 3 73.338 41.152 6.254 0.5 51.5 ? C4 PDP 860 B 1 HETATM 12 C C4 PDP . B . H 3 73.397 41.172 6.265 0.5 50.17 ? C4 PDP 860 B 1 HETATM 13 C C4A PDP . A . H 3 74.254 40.544 5.407 0.5 47.12 ? C4A PDP 860 B 1 HETATM 14 C C4A PDP . B . H 3 74.31 40.578 5.391 0.5 45.45 ? C4A PDP 860 B 1 HETATM 15 C C5 PDP . A . H 3 73.086 42.511 6.14 0.5 53.61 ? C5 PDP 860 B 1 HETATM 16 C C5 PDP . B . H 3 73.102 42.52 6.146 0.5 51.33 ? C5 PDP 860 B 1 HETATM 17 C C6 PDP . A . H 3 72.075 43.078 6.859 0.5 53 ? C6 PDP 860 B 1 HETATM 18 C C6 PDP . B . H 3 72.073 43.056 6.859 0.5 51.28 ? C6 PDP 860 B 1 HETATM 19 C C5A PDP . A . H 3 73.765 43.355 5.066 0.5 58.85 ? C5A PDP 860 B 1 HETATM 20 C C5A PDP . B . H 3 73.821 43.428 5.132 0.5 56.82 ? C5A PDP 860 B 1 HETATM 21 O O5A PDP . A . H 3 73.203 43.097 3.774 0.5 65.54 ? O5A PDP 860 B 1 HETATM 22 O O5A PDP . B . H 3 73.708 43.276 3.7 0.5 62.44 ? O5A PDP 860 B 1 HETATM 23 P PA PDP . A . H 3 72.606 44.138 2.916 0.5 67.7 ? PA PDP 860 B 1 HETATM 24 P PA PDP . B . H 3 72.547 43.496 2.801 0.5 65.55 ? PA PDP 860 B 1 HETATM 25 O O1A PDP . A . H 3 71.107 43.693 2.626 0.5 71.84 ? O1A PDP 860 B 1 HETATM 26 O O1A PDP . B . H 3 71.206 42.894 3.447 0.5 66.49 ? O1A PDP 860 B 1 HETATM 27 O O3A PDP . A . H 3 72.558 45.549 3.369 0.5 69.09 ? O3A PDP 860 B 1 HETATM 28 O O3A PDP . B . H 3 72.297 44.796 2.182 0.5 68.41 ? O3A PDP 860 B 1 HETATM 29 O O2A PDP . A . H 3 73.232 43.918 1.468 0.5 68.93 ? O2A PDP 860 B 1 HETATM 30 O O2A PDP . B . H 3 72.79 42.553 1.566 0.5 66.87 ? O2A PDP 860 B 1 HETATM 31 P PB PDP . A . H 3 73.444 46.562 2.743 0.5 69.3 ? PB PDP 860 B 1 HETATM 32 P PB PDP . B . H 3 71.717 45.816 3.102 0.5 67.12 ? PB PDP 860 B 1 HETATM 33 O O1B PDP . A . H 3 74.95 45.95 2.741 0.5 69.53 ? O1B PDP 860 B 1 HETATM 34 O O1B PDP . B . H 3 70.136 45.461 2.999 0.5 68.79 ? O1B PDP 860 B 1 HETATM 35 O O2B PDP . A . H 3 73.166 46.862 1.32 0.5 67.27 ? O2B PDP 860 B 1 HETATM 36 O O2B PDP . B . H 3 71.946 45.648 4.558 0.5 63.6 ? O2B PDP 860 B 1 HETATM 37 O O3B PDP . A . H 3 73.659 47.761 3.58 0.5 66.61 ? O3B PDP 860 B 1 HETATM 38 O O3B PDP . B . H 3 71.702 47.228 2.673 0.5 64.34 ? O3B PDP 860 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #