data_6M5W # _model_server_result.job_id 3jgw0LCgoKAjL21yohroIw _model_server_result.datetime_utc '2025-02-18 09:01:47' _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 6m5w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6M5W # _exptl.entry_id 6M5W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _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 120 _cell.entry_id 6M5W _cell.length_a 152.749 _cell.length_b 152.749 _cell.length_c 235.933 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6M5W _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 76.3745 132.284514 0 3 'crystal symmetry operation' 7_556 y,x,-z+5/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 393.221667 4 'crystal symmetry operation' 10_666 -y+1,-x+1,-z+5/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 76.3745 132.284514 393.221667 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id C _struct_conn.ptnr1_label_atom_id C23 _struct_conn.ptnr1_label_comp_id DXC _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id DXC _struct_conn.ptnr1_auth_seq_id 502 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id GLY _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id GLY _struct_conn.ptnr2_auth_seq_id 503 _struct_conn.ptnr2_symmetry 1_555 _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 1.33 _struct_conn.pdbx_value_order ? # _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 329 n y N1 C6 PLP sing 330 n y C2 C2A PLP sing 331 n n C2 C3 PLP sing 332 n y C2A H2A1 PLP sing 333 n n C2A H2A2 PLP sing 334 n n C2A H2A3 PLP sing 335 n n C3 O3 PLP sing 336 n n C3 C4 PLP doub 337 n y O3 HO3 PLP sing 338 n n C4 C4A PLP sing 339 n n C4 C5 PLP sing 340 n y C4A O4A PLP doub 341 n n C4A H4A PLP sing 342 n n C5 C6 PLP doub 343 n y C5 C5A PLP sing 344 n n C6 H6 PLP sing 345 n n C5A O4P PLP sing 346 n n C5A H5A1 PLP sing 347 n n C5A H5A2 PLP sing 348 n n O4P P PLP sing 349 n n P O1P PLP doub 350 n n P O2P PLP sing 351 n n P O3P PLP sing 352 n n O2P HOP2 PLP sing 353 n n O3P HOP3 PLP sing 354 n n # _atom_sites.entry_id 6M5W _atom_sites.fract_transf_matrix[1][1] 0.006547 _atom_sites.fract_transf_matrix[1][2] 0.00378 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007559 _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] 0.004238 _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 PLP A 1 501 500 PLP PLP . C 3 DXC A 1 502 601 DXC DCA . D 4 GLY A 1 503 601 GLY DCA . # 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 . . . B 2 57.728 56.164 183.093 1 20.99 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . B 2 58.084 55.284 182.094 1 20.36 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . B 2 57.975 55.713 180.66 1 23.51 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . B 2 58.545 54.01 182.42 1 27.28 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . B 2 58.898 53.135 181.428 1 35.99 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . B 2 58.636 53.601 183.747 1 31.49 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . B 2 58.426 52.132 183.983 1 35.73 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . B 2 58.279 54.506 184.751 1 26.09 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . B 2 57.826 55.776 184.411 1 21.82 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . B 2 58.36 54.171 186.226 1 26.35 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . B 2 58.331 52.794 186.515 1 23.21 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . B 2 59.219 52.225 187.732 1 21.82 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . B 2 59.355 50.721 187.632 1 29.45 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . B 2 60.583 52.874 187.664 1 25.43 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . B 2 58.556 52.6 189.039 1 18 ? O3P PLP 501 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #