data_4ZGY # _model_server_result.job_id yN-Qa_KSeTgLtd9e6aJLMw _model_server_result.datetime_utc '2024-12-12 08:00:48' _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 4zgy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4ZGY # _exptl.entry_id 4ZGY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 4ZGY _cell.length_a 51.698 _cell.length_b 73.368 _cell.length_c 162.084 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZGY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,F _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 NZ LYS 70 A LYS 69 1_555 C C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.306 ? metalc ? metalc1 A O PHE 239 A PHE 238 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc2 C O1P PLP . A PLP 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 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 N1 C2 PLP doub 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 4ZGY _atom_sites.fract_transf_matrix[1][1] 0.019343 _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] 0.01363 _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] 0.00617 _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 C 3 PLP A 1 501 501 PLP PLP . D 4 MG A 1 502 502 MG MG . E 5 HOH A 1 601 610 HOH HOH . E 5 HOH A 2 602 605 HOH HOH . E 5 HOH A 3 603 603 HOH HOH . E 5 HOH A 4 604 611 HOH HOH . E 5 HOH A 5 605 604 HOH HOH . E 5 HOH A 6 606 612 HOH HOH . E 5 HOH A 7 607 602 HOH HOH . E 5 HOH A 8 608 608 HOH HOH . E 5 HOH A 9 609 606 HOH HOH . E 5 HOH A 10 610 607 HOH HOH . E 5 HOH A 11 611 609 HOH HOH . E 5 HOH A 12 612 601 HOH HOH . F 5 HOH B 1 301 301 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 N1 PLP . . . C 3 12.154 -0.631 11.751 1 82.79 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . C 3 13.006 0.429 11.844 1 90.69 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . C 3 14.115 0.597 10.861 1 91.51 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . C 3 12.847 1.361 12.858 1 92.6 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . C 3 13.708 2.431 12.954 1 96.54 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . C 3 11.837 1.221 13.769 1 86.44 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . C 3 11.692 2.243 14.849 1 78.62 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . C 3 10.976 0.153 13.678 1 82.67 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . C 3 11.143 -0.778 12.656 1 81.14 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . C 3 9.874 0.011 14.676 1 72.69 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . C 3 8.964 -0.961 14.325 1 69.6 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . C 3 7.65 -1.081 15.159 1 64.32 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . C 3 6.818 -2.249 14.663 1 69.36 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . C 3 6.848 0.192 15.026 1 69.44 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . C 3 8.009 -1.275 16.614 1 57.68 ? O3P PLP 501 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #