data_5AFU # _model_server_result.job_id Syu7vuogOEAJqwQ8J-wJBg _model_server_result.datetime_utc '2025-02-05 08:58:25' _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":"LA","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 . . . LA 23 5.047 5.463 12.97 1 38.46 ? PB ADP 800 E 1 HETATM 2 O O1B ADP . . . LA 23 3.826 6.197 13.473 1 37.96 ? O1B ADP 800 E 1 HETATM 3 O O2B ADP . . . LA 23 6.177 6.358 12.521 1 38.18 -1 O2B ADP 800 E 1 HETATM 4 O O3B ADP . . . LA 23 5.481 4.313 13.848 1 38.6 ? O3B ADP 800 E 1 HETATM 5 P PA ADP . . . LA 23 3.653 5.505 10.524 1 35.91 ? PA ADP 800 E 1 HETATM 6 O O1A ADP . . . LA 23 2.219 5.369 10.968 1 36.04 -1 O1A ADP 800 E 1 HETATM 7 O O2A ADP . . . LA 23 4.216 6.888 10.296 1 35.7 ? O2A ADP 800 E 1 HETATM 8 O O3A ADP . . . LA 23 4.572 4.745 11.608 1 37.06 ? O3A ADP 800 E 1 HETATM 9 O O5' ADP . . . LA 23 3.857 4.595 9.207 1 36.47 ? O5' ADP 800 E 1 HETATM 10 C C5' ADP . . . LA 23 4.765 4.925 8.153 1 37.08 ? C5' ADP 800 E 1 HETATM 11 C C4' ADP . . . LA 23 5.603 3.706 7.786 1 37.3 ? C4' ADP 800 E 1 HETATM 12 O O4' ADP . . . LA 23 4.803 2.727 7.115 1 36.65 ? O4' ADP 800 E 1 HETATM 13 C C3' ADP . . . LA 23 6.756 4.072 6.859 1 37.71 ? C3' ADP 800 E 1 HETATM 14 O O3' ADP . . . LA 23 8.006 4.046 7.561 1 37.89 ? O3' ADP 800 E 1 HETATM 15 C C2' ADP . . . LA 23 6.703 3.062 5.725 1 37.49 ? C2' ADP 800 E 1 HETATM 16 O O2' ADP . . . LA 23 7.736 2.077 5.847 1 37.44 ? O2' ADP 800 E 1 HETATM 17 C C1' ADP . . . LA 23 5.328 2.407 5.824 1 36.72 ? C1' ADP 800 E 1 HETATM 18 N N9 ADP . . . LA 23 4.401 2.911 4.772 1 35.72 ? N9 ADP 800 E 1 HETATM 19 C C8 ADP . . . LA 23 4.157 4.207 4.483 1 35.46 ? C8 ADP 800 E 1 HETATM 20 N N7 ADP . . . LA 23 3.259 4.319 3.47 1 35.2 ? N7 ADP 800 E 1 HETATM 21 C C5 ADP . . . LA 23 2.906 3.077 3.098 1 35.21 ? C5 ADP 800 E 1 HETATM 22 C C6 ADP . . . LA 23 2 2.478 2.083 1 35.87 ? C6 ADP 800 E 1 HETATM 23 N N6 ADP . . . LA 23 1.267 3.258 1.251 1 36.64 ? N6 ADP 800 E 1 HETATM 24 N N1 ADP . . . LA 23 1.923 1.124 2.023 1 35.7 ? N1 ADP 800 E 1 HETATM 25 C C2 ADP . . . LA 23 2.643 0.327 2.845 1 36 ? C2 ADP 800 E 1 HETATM 26 N N3 ADP . . . LA 23 3.488 0.81 3.786 1 35.59 ? N3 ADP 800 E 1 HETATM 27 C C4 ADP . . . LA 23 3.663 2.148 3.959 1 35.12 ? C4 ADP 800 E 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 277 _model_server_stats.query_time_ms 374 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #