data_1ABB # _model_server_result.job_id DnVE3v4USjuRe8QUBgmb6Q _model_server_result.datetime_utc '2024-10-13 19:18:06' _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 1abb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":931}' # _entry.id 1ABB # _exptl.entry_id 1ABB _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 109.29 _cell.angle_gamma 90 _cell.entry_id 1ABB _cell.length_a 119 _cell.length_b 188.1 _cell.length_c 88.1 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ABB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _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,M,N,O,P _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 I N N ? 3 L N N ? 3 O 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 671 A LYS 680 1_555 F C4A PDP . A PDP 931 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale2 B NZ LYS 671 B LYS 680 1_555 I C4A PDP . B PDP 932 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale3 C NZ LYS 671 C LYS 680 1_555 L C4A PDP . C PDP 933 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale4 D NZ LYS 671 D LYS 680 1_555 O C4A PDP . D PDP 934 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? # _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 273 n y N1 C6 PDP sing 274 n y C2 C2A PDP sing 275 n n C2 C3 PDP sing 276 n y C2A H2A1 PDP sing 277 n n C2A H2A2 PDP sing 278 n n C2A H2A3 PDP sing 279 n n C3 O3 PDP sing 280 n n C3 C4 PDP doub 281 n y O3 HO3 PDP sing 282 n n C4 C4A PDP sing 283 n n C4 C5 PDP sing 284 n y C4A O4A PDP doub 285 n n C4A H4A PDP sing 286 n n C5 C6 PDP doub 287 n y C5 C5A PDP sing 288 n n C6 H6 PDP sing 289 n n C5A O5A PDP sing 290 n n C5A H5A1 PDP sing 291 n n C5A H5A2 PDP sing 292 n n O5A PA PDP sing 293 n n PA O1A PDP doub 294 n n PA O3A PDP sing 295 n n PA O2A PDP sing 296 n n O3A PB PDP sing 297 n n O2A HOA2 PDP sing 298 n n PB O1B PDP doub 299 n n PB O2B PDP sing 300 n n PB O3B PDP sing 301 n n O2B HOB2 PDP sing 302 n n O3B HOB3 PDP sing 303 n n # _atom_sites.entry_id 1ABB _atom_sites.fract_transf_matrix[1][1] 0.008403 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002941 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005316 _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] 0.012026 _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 SO4 A 1 900 900 SO4 SO4 . F 3 PDP A 1 931 931 PDP PDP . G 4 IMP A 1 920 920 IMP IMP . H 2 SO4 B 1 900 900 SO4 SO4 . I 3 PDP B 1 932 932 PDP PDP . J 4 IMP B 1 920 920 IMP IMP . K 2 SO4 C 1 900 900 SO4 SO4 . L 3 PDP C 1 933 933 PDP PDP . M 4 IMP C 1 920 920 IMP IMP . N 2 SO4 D 1 900 900 SO4 SO4 . O 3 PDP D 1 934 934 PDP PDP . P 4 IMP D 1 920 920 IMP IMP . # 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 . . . F 3 41.414 3.391 29.326 1 4.2 ? N1 PDP 931 A 1 HETATM 2 C C2 PDP . . . F 3 40.922 2.422 30.122 1 2 ? C2 PDP 931 A 1 HETATM 3 C C2A PDP . . . F 3 40.717 2.678 31.575 1 4.54 ? C2A PDP 931 A 1 HETATM 4 C C3 PDP . . . F 3 40.549 1.209 29.571 1 2.78 ? C3 PDP 931 A 1 HETATM 5 O O3 PDP . . . F 3 40.112 0.178 30.408 1 10.31 ? O3 PDP 931 A 1 HETATM 6 C C4 PDP . . . F 3 40.681 0.98 28.227 1 3.09 ? C4 PDP 931 A 1 HETATM 7 C C4A PDP . . . F 3 40.191 -0.29 27.603 1 2 ? C4A PDP 931 A 1 HETATM 8 C C5 PDP . . . F 3 41.215 1.952 27.405 1 4.92 ? C5 PDP 931 A 1 HETATM 9 C C6 PDP . . . F 3 41.557 3.194 27.982 1 3.39 ? C6 PDP 931 A 1 HETATM 10 C C5A PDP . . . F 3 41.212 1.798 25.954 1 9.98 ? C5A PDP 931 A 1 HETATM 11 O O5A PDP . . . F 3 40.398 2.906 25.428 1 22.25 ? O5A PDP 931 A 1 HETATM 12 P PA PDP . . . F 3 39.956 3.348 23.924 1 21.11 ? PA PDP 931 A 1 HETATM 13 O O1A PDP . . . F 3 38.483 3.179 23.966 1 25.95 ? O1A PDP 931 A 1 HETATM 14 O O3A PDP . . . F 3 40.085 4.937 23.425 1 41.49 ? O3A PDP 931 A 1 HETATM 15 O O2A PDP . . . F 3 40.621 2.495 22.897 1 25.86 ? O2A PDP 931 A 1 HETATM 16 P PB PDP . . . F 3 41.487 5.82 23.427 1 65.77 ? PB PDP 931 A 1 HETATM 17 O O1B PDP . . . F 3 41.138 6.976 22.566 1 61.31 ? O1B PDP 931 A 1 HETATM 18 O O2B PDP . . . F 3 41.658 6.257 24.844 1 62.04 ? O2B PDP 931 A 1 HETATM 19 O O3B PDP . . . F 3 42.608 4.97 22.87 1 65.68 ? O3B PDP 931 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #