data_5AFU # _model_server_result.job_id bh85mkaCqjf94yRsJkTISg _model_server_result.datetime_utc '2024-10-14 05:20:46' _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 5afu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"NA","auth_seq_id":800}' # _entry.id 5AFU # _exptl.entry_id 5AFU _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 23 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 9 _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 5AFU _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AFU _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 33-meric _pdbx_struct_assembly.oligomeric_count 33 _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,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA _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 ? 23 HA N N ? 23 IA N N ? 23 JA N N ? 23 KA N N ? 23 LA N N ? 23 MA N N ? 23 NA N N ? 23 PA N N ? 23 QA N N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 5AFU _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 HA 23 ADP A 1 800 800 ADP ADP . IA 23 ADP B 1 800 800 ADP ADP . JA 23 ADP C 1 800 800 ADP ADP . KA 23 ADP D 1 800 800 ADP ADP . LA 23 ADP E 1 800 800 ADP ADP . MA 23 ADP F 1 800 800 ADP ADP . NA 23 ADP G 1 800 800 ADP ADP . OA 24 ATP H 1 401 401 ATP ATP . PA 23 ADP I 1 800 800 ADP ADP . QA 23 ADP J 1 800 800 ADP ADP . # 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 P PB ADP . . . NA 23 48.701 20.075 -18.401 1 36.39 ? PB ADP 800 G 1 HETATM 2 O O1B ADP . . . NA 23 48.02 21.086 -17.506 1 36.13 ? O1B ADP 800 G 1 HETATM 3 O O2B ADP . . . NA 23 50.123 20.429 -18.764 1 36.53 -1 O2B ADP 800 G 1 HETATM 4 O O3B ADP . . . NA 23 48.515 18.642 -17.961 1 36.61 ? O3B ADP 800 G 1 HETATM 5 P PA ADP . . . NA 23 46.689 21.119 -20.109 1 33.82 ? PA ADP 800 G 1 HETATM 6 O O1A ADP . . . NA 23 45.534 20.667 -19.248 1 33.62 -1 O1A ADP 800 G 1 HETATM 7 O O2A ADP . . . NA 23 47.17 22.548 -20.013 1 34.31 ? O2A ADP 800 G 1 HETATM 8 O O3A ADP . . . NA 23 47.935 20.138 -19.821 1 34.92 ? O3A ADP 800 G 1 HETATM 9 O O5' ADP . . . NA 23 46.342 20.784 -21.649 1 34.27 ? O5' ADP 800 G 1 HETATM 10 C C5' ADP . . . NA 23 47.147 21.26 -22.731 1 34.84 ? C5' ADP 800 G 1 HETATM 11 C C4' ADP . . . NA 23 47.613 20.09 -23.595 1 35.43 ? C4' ADP 800 G 1 HETATM 12 O O4' ADP . . . NA 23 46.547 19.624 -24.43 1 35.4 ? O4' ADP 800 G 1 HETATM 13 C C3' ADP . . . NA 23 48.772 20.474 -24.511 1 36.09 ? C3' ADP 800 G 1 HETATM 14 O O3' ADP . . . NA 23 50.009 19.934 -24.029 1 36.67 ? O3' ADP 800 G 1 HETATM 15 C C2' ADP . . . NA 23 48.402 19.938 -25.885 1 35.94 ? C2' ADP 800 G 1 HETATM 16 O O2' ADP . . . NA 23 49.128 18.745 -26.204 1 35.94 ? O2' ADP 800 G 1 HETATM 17 C C1' ADP . . . NA 23 46.906 19.645 -25.815 1 35.38 ? C1' ADP 800 G 1 HETATM 18 N N9 ADP . . . NA 23 46.119 20.689 -26.529 1 34.83 ? N9 ADP 800 G 1 HETATM 19 C C8 ADP . . . NA 23 46.187 22.021 -26.315 1 34.76 ? C8 ADP 800 G 1 HETATM 20 N N7 ADP . . . NA 23 45.337 22.689 -27.137 1 34.96 ? N7 ADP 800 G 1 HETATM 21 C C5 ADP . . . NA 23 44.7 21.781 -27.895 1 35.22 ? C5 ADP 800 G 1 HETATM 22 C C6 ADP . . . NA 23 43.676 21.808 -28.974 1 35.71 ? C6 ADP 800 G 1 HETATM 23 N N6 ADP . . . NA 23 43.143 22.976 -29.406 1 36 ? N6 ADP 800 G 1 HETATM 24 N N1 ADP . . . NA 23 43.285 20.622 -29.505 1 35.32 ? N1 ADP 800 G 1 HETATM 25 C C2 ADP . . . NA 23 43.801 19.443 -29.088 1 35.17 ? C2 ADP 800 G 1 HETATM 26 N N3 ADP . . . NA 23 44.738 19.351 -28.117 1 35.25 ? N3 ADP 800 G 1 HETATM 27 C C4 ADP . . . NA 23 45.223 20.46 -27.494 1 35.03 ? C4 ADP 800 G 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 99 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #