data_6YMH # _model_server_result.job_id CFGPLencO4kXL5vW0dlxCQ _model_server_result.datetime_utc '2024-12-23 09:52:40' _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 6ymh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":302}' # _entry.id 6YMH # _exptl.entry_id 6YMH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 4 _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 6YMH _cell.length_a 54.164 _cell.length_b 54.164 _cell.length_c 271.968 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YMH _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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,G,H _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 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 314 n y N1 C6 PLP sing 315 n y C2 C2A PLP sing 316 n n C2 C3 PLP sing 317 n y C2A H2A1 PLP sing 318 n n C2A H2A2 PLP sing 319 n n C2A H2A3 PLP sing 320 n n C3 O3 PLP sing 321 n n C3 C4 PLP doub 322 n y O3 HO3 PLP sing 323 n n C4 C4A PLP sing 324 n n C4 C5 PLP sing 325 n y C4A O4A PLP doub 326 n n C4A H4A PLP sing 327 n n C5 C6 PLP doub 328 n y C5 C5A PLP sing 329 n n C6 H6 PLP sing 330 n n C5A O4P PLP sing 331 n n C5A H5A1 PLP sing 332 n n C5A H5A2 PLP sing 333 n n O4P P PLP sing 334 n n P O1P PLP doub 335 n n P O2P PLP sing 336 n n P O3P PLP sing 337 n n O2P HOP2 PLP sing 338 n n O3P HOP3 PLP sing 339 n n # _atom_sites.entry_id 6YMH _atom_sites.fract_transf_matrix[1][1] 0.018462 _atom_sites.fract_transf_matrix[1][2] 0.010659 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021319 _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] 0.003677 _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 2 FMN AAA 1 301 250 FMN FMN . D 3 SO4 AAA 1 302 1 SO4 SO4 . E 2 FMN BBB 1 301 250 FMN FMN . F 4 PLP BBB 1 302 1 PLP PLP . G 5 HOH AAA 1 401 4 HOH HOH . G 5 HOH AAA 2 402 68 HOH HOH . G 5 HOH AAA 3 403 31 HOH HOH . G 5 HOH AAA 4 404 123 HOH HOH . G 5 HOH AAA 5 405 79 HOH HOH . G 5 HOH AAA 6 406 162 HOH HOH . G 5 HOH AAA 7 407 35 HOH HOH . G 5 HOH AAA 8 408 5 HOH HOH . G 5 HOH AAA 9 409 122 HOH HOH . G 5 HOH AAA 10 410 149 HOH HOH . G 5 HOH AAA 11 411 86 HOH HOH . G 5 HOH AAA 12 412 98 HOH HOH . G 5 HOH AAA 13 413 147 HOH HOH . G 5 HOH AAA 14 414 71 HOH HOH . G 5 HOH AAA 15 415 56 HOH HOH . H 5 HOH BBB 1 401 24 HOH HOH . H 5 HOH BBB 2 402 66 HOH HOH . H 5 HOH BBB 3 403 20 HOH HOH . H 5 HOH BBB 4 404 6 HOH HOH . H 5 HOH BBB 5 405 176 HOH HOH . H 5 HOH BBB 6 406 52 HOH HOH . H 5 HOH BBB 7 407 27 HOH HOH . H 5 HOH BBB 8 408 43 HOH HOH . H 5 HOH BBB 9 409 21 HOH HOH . H 5 HOH BBB 10 410 115 HOH HOH . H 5 HOH BBB 11 411 39 HOH HOH . H 5 HOH BBB 12 412 29 HOH HOH . H 5 HOH BBB 13 413 23 HOH HOH . H 5 HOH BBB 14 414 22 HOH HOH . H 5 HOH BBB 15 415 3 HOH HOH . H 5 HOH BBB 16 416 34 HOH HOH . H 5 HOH BBB 17 417 107 HOH HOH . H 5 HOH BBB 18 418 41 HOH HOH . H 5 HOH BBB 19 419 55 HOH HOH . H 5 HOH BBB 20 420 177 HOH HOH . H 5 HOH BBB 21 421 37 HOH HOH . H 5 HOH BBB 22 422 92 HOH HOH . H 5 HOH BBB 23 423 28 HOH HOH . H 5 HOH BBB 24 424 80 HOH HOH . H 5 HOH BBB 25 425 125 HOH HOH . H 5 HOH BBB 26 426 57 HOH HOH . H 5 HOH BBB 27 427 128 HOH HOH . H 5 HOH BBB 28 428 53 HOH HOH . H 5 HOH BBB 29 429 126 HOH HOH . H 5 HOH BBB 30 430 87 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 . . . F 4 -37.226 41.363 -10.291 0.81 86.68 ? N1 PLP 302 BBB 1 HETATM 2 C C2 PLP . . . F 4 -36.563 42.276 -11.047 0.81 90 ? C2 PLP 302 BBB 1 HETATM 3 C C2A PLP . . . F 4 -35.372 43.005 -10.51 0.81 87.47 ? C2A PLP 302 BBB 1 HETATM 4 C C3 PLP . . . F 4 -37.007 42.565 -12.434 0.81 93.99 ? C3 PLP 302 BBB 1 HETATM 5 O O3 PLP . . . F 4 -36.336 43.479 -13.195 0.81 94.71 ? O3 PLP 302 BBB 1 HETATM 6 C C4 PLP . . . F 4 -38.196 41.828 -12.95 0.81 91.47 ? C4 PLP 302 BBB 1 HETATM 7 C C4A PLP . . . F 4 -38.668 42.074 -14.34 0.81 90.71 ? C4A PLP 302 BBB 1 HETATM 8 O O4A PLP . . . F 4 -38.039 42.838 -15.052 0.81 90.65 ? O4A PLP 302 BBB 1 HETATM 9 C C5 PLP . . . F 4 -38.843 40.855 -12.008 0.81 84.57 ? C5 PLP 302 BBB 1 HETATM 10 C C6 PLP . . . F 4 -38.304 40.683 -10.732 0.81 84.92 ? C6 PLP 302 BBB 1 HETATM 11 C C5A PLP . . . F 4 -40.052 40.033 -12.387 0.81 80.4 ? C5A PLP 302 BBB 1 HETATM 12 O O4P PLP . . . F 4 -41.004 39.995 -11.325 0.81 75.91 ? O4P PLP 302 BBB 1 HETATM 13 P P PLP . . . F 4 -42.363 39.144 -11.468 0.81 73.73 ? P PLP 302 BBB 1 HETATM 14 O O1P PLP . . . F 4 -42.124 38.382 -12.751 0.81 73.36 ? O1P PLP 302 BBB 1 HETATM 15 O O2P PLP . . . F 4 -42.436 38.349 -10.198 0.81 73.93 ? O2P PLP 302 BBB 1 HETATM 16 O O3P PLP . . . F 4 -43.507 40.115 -11.532 0.81 83.62 ? O3P PLP 302 BBB 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #