data_1PYG # _model_server_result.job_id B4KnqQBAo_w2c_WkyC66Qw _model_server_result.datetime_utc '2025-02-05 11:55:21' _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":"F","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 . F 3 69.136 44.269 65.869 0.5 51.91 ? N1 PDP 860 A 1 HETATM 2 N N1 PDP . B . F 3 69.229 44.113 65.98 0.5 50.48 ? N1 PDP 860 A 1 HETATM 3 C C2 PDP . A . F 3 70.347 43.655 65.865 0.5 51.89 ? C2 PDP 860 A 1 HETATM 4 C C2 PDP . B . F 3 70.339 43.346 66.063 0.5 50.93 ? C2 PDP 860 A 1 HETATM 5 C C2A PDP . A . F 3 71.466 44.275 65.094 0.5 51.09 ? C2A PDP 860 A 1 HETATM 6 C C2A PDP . B . F 3 71.621 43.82 65.362 0.5 50.4 ? C2A PDP 860 A 1 HETATM 7 C C3 PDP . A . F 3 70.593 42.589 66.692 0.5 51.2 ? C3 PDP 860 A 1 HETATM 8 C C3 PDP . B . F 3 70.355 42.284 66.896 0.5 49.91 ? C3 PDP 860 A 1 HETATM 9 O O3 PDP . A . F 3 71.754 41.868 66.526 0.5 51.43 ? O3 PDP 860 A 1 HETATM 10 O O3 PDP . B . F 3 71.452 41.462 66.905 0.5 50.56 ? O3 PDP 860 A 1 HETATM 11 C C4 PDP . A . F 3 69.624 42.187 67.58 0.5 49.3 ? C4 PDP 860 A 1 HETATM 12 C C4 PDP . B . F 3 69.265 42.011 67.713 0.5 47.88 ? C4 PDP 860 A 1 HETATM 13 C C4A PDP . A . F 3 70.012 41.407 68.699 0.5 43.02 ? C4A PDP 860 A 1 HETATM 14 C C4A PDP . B . F 3 69.302 41.006 68.694 0.5 42.48 ? C4A PDP 860 A 1 HETATM 15 C C5 PDP . A . F 3 68.383 42.817 67.578 0.5 52.25 ? C5 PDP 860 A 1 HETATM 16 C C5 PDP . B . F 3 68.166 42.849 67.652 0.5 49.82 ? C5 PDP 860 A 1 HETATM 17 C C6 PDP . A . F 3 68.155 43.834 66.711 0.5 51.7 ? C6 PDP 860 A 1 HETATM 18 C C6 PDP . B . F 3 68.149 43.888 66.758 0.5 49.87 ? C6 PDP 860 A 1 HETATM 19 C C5A PDP . A . F 3 67.382 42.636 68.759 0.5 55.88 ? C5A PDP 860 A 1 HETATM 20 C C5A PDP . B . F 3 67.104 42.81 68.763 0.5 52.58 ? C5A PDP 860 A 1 HETATM 21 O O5A PDP . A . F 3 67.601 43.698 69.689 0.5 62.32 ? O5A PDP 860 A 1 HETATM 22 O O5A PDP . B . F 3 67.482 43.807 69.715 0.5 56.74 ? O5A PDP 860 A 1 HETATM 23 P PA PDP . A . F 3 66.586 44.272 70.609 0.5 64.77 ? PA PDP 860 A 1 HETATM 24 P PA PDP . B . F 3 66.562 44.415 70.703 0.5 58.07 ? PA PDP 860 A 1 HETATM 25 O O1A PDP . A . F 3 67.406 45.131 71.685 0.5 66.69 ? O1A PDP 860 A 1 HETATM 26 O O1A PDP . B . F 3 67.461 45.236 71.731 0.5 59.87 ? O1A PDP 860 A 1 HETATM 27 O O3A PDP . A . F 3 65.44 45.087 70.107 0.5 66.94 ? O3A PDP 860 A 1 HETATM 28 O O3A PDP . B . F 3 65.347 45.142 70.264 0.5 59.66 ? O3A PDP 860 A 1 HETATM 29 O O2A PDP . A . F 3 66.134 43.073 71.572 0.5 66.04 ? O2A PDP 860 A 1 HETATM 30 O O2A PDP . B . F 3 66.084 43.202 71.634 0.5 60.17 ? O2A PDP 860 A 1 HETATM 31 P PB PDP . A . F 3 64.076 44.526 70.249 0.5 71.66 ? PB PDP 860 A 1 HETATM 32 P PB PDP . B . F 3 65.414 46.618 70.092 0.5 61.2 ? PB PDP 860 A 1 HETATM 33 O O1B PDP . A . F 3 63.236 45.582 69.351 0.5 67 ? O1B PDP 860 A 1 HETATM 34 O O1B PDP . B . F 3 66.928 47.027 69.696 0.5 60.2 ? O1B PDP 860 A 1 HETATM 35 O O2B PDP . A . F 3 63.841 43.234 69.554 0.5 70.53 ? O2B PDP 860 A 1 HETATM 36 O O2B PDP . B . F 3 64.68 47.087 68.901 0.5 59.18 ? O2B PDP 860 A 1 HETATM 37 O O3B PDP . A . F 3 63.459 44.666 71.593 0.5 69.05 ? O3B PDP 860 A 1 HETATM 38 O O3B PDP . B . F 3 65.18 47.434 71.307 0.5 61.09 ? O3B PDP 860 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 375 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #