data_9DH3 # _model_server_result.job_id AzwzylTY4rdqki9DQCyB2A _model_server_result.datetime_utc '2025-02-26 08:57:47' _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 9dh3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1101}' # _entry.id 9DH3 # _exptl.entry_id 9DH3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-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 90 _cell.angle_gamma 90 _cell.entry_id 9DH3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DH3 _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 ? _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 ? 2 E N N ? 2 H N N ? 2 K N N ? 2 N 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 43 n n PB O2B ADP sing 44 n n PB O3B ADP sing 45 n n PB O3A ADP sing 46 n n O2B HOB2 ADP sing 47 n n O3B HOB3 ADP sing 48 n n PA O1A ADP doub 49 n n PA O2A ADP sing 50 n n PA O3A ADP sing 51 n n PA O5' ADP sing 52 n n O2A HOA2 ADP sing 53 n n O5' C5' ADP sing 54 n n C5' C4' ADP sing 55 n n C5' "H5'1" ADP sing 56 n n C5' "H5'2" ADP sing 57 n n C4' O4' ADP sing 58 n n C4' C3' ADP sing 59 n n C4' H4' ADP sing 60 n n O4' C1' ADP sing 61 n n C3' O3' ADP sing 62 n n C3' C2' ADP sing 63 n n C3' H3' ADP sing 64 n n O3' HO3' ADP sing 65 n n C2' O2' ADP sing 66 n n C2' C1' ADP sing 67 n n C2' H2' ADP sing 68 n n O2' HO2' ADP sing 69 n n C1' N9 ADP sing 70 n n C1' H1' ADP sing 71 n n N9 C8 ADP sing 72 n y N9 C4 ADP sing 73 n y C8 N7 ADP doub 74 n y C8 H8 ADP sing 75 n n N7 C5 ADP sing 76 n y C5 C6 ADP sing 77 n y C5 C4 ADP doub 78 n y C6 N6 ADP sing 79 n n C6 N1 ADP doub 80 n y N6 HN61 ADP sing 81 n n N6 HN62 ADP sing 82 n n N1 C2 ADP sing 83 n y C2 N3 ADP doub 84 n y C2 H2 ADP sing 85 n n N3 C4 ADP sing 86 n y # _atom_sites.entry_id 9DH3 _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 E 2 ADP A 1 1101 1039 ADP ADP . F 3 A1A4L A 1 1102 1139 A1A4L LIG . G 4 CPS A 1 1103 1239 CPS CPS . H 2 ADP B 1 1101 1039 ADP ADP . I 3 A1A4L B 1 1102 1139 A1A4L LIG . J 4 CPS B 1 1103 1239 CPS CPS . K 2 ADP C 1 1101 1039 ADP ADP . L 3 A1A4L C 1 1102 1139 A1A4L LIG . M 4 CPS C 1 1103 1239 CPS CPS . N 2 ADP D 1 1101 1039 ADP ADP . O 3 A1A4L D 1 1102 1139 A1A4L LIG . P 4 CPS D 1 1103 1239 CPS CPS . # 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 . . . H 2 190.037 172.261 188.455 1 49.16 ? PB ADP 1101 B 1 HETATM 2 O O1B ADP . . . H 2 190.829 171.253 189.225 1 49.27 ? O1B ADP 1101 B 1 HETATM 3 O O2B ADP . . . H 2 190.8 173.514 188.144 1 49.1 -1 O2B ADP 1101 B 1 HETATM 4 O O3B ADP . . . H 2 189.414 171.684 187.217 1 39.57 ? O3B ADP 1101 B 1 HETATM 5 P PA ADP . . . H 2 187.444 173.363 189.127 1 31.55 ? PA ADP 1101 B 1 HETATM 6 O O1A ADP . . . H 2 187.682 174.643 188.399 1 28.15 -1 O1A ADP 1101 B 1 HETATM 7 O O2A ADP . . . H 2 186.534 172.368 188.491 1 29.55 ? O2A ADP 1101 B 1 HETATM 8 O O3A ADP . . . H 2 188.835 172.674 189.424 1 35.32 ? O3A ADP 1101 B 1 HETATM 9 O O5' ADP . . . H 2 186.899 173.711 190.609 1 25.32 ? O5' ADP 1101 B 1 HETATM 10 C C5' ADP . . . H 2 185.495 174.083 190.774 1 24.99 ? C5' ADP 1101 B 1 HETATM 11 C C4' ADP . . . H 2 185.26 174.808 192.091 1 25.63 ? C4' ADP 1101 B 1 HETATM 12 O O4' ADP . . . H 2 183.82 175.054 192.234 1 23.58 ? O4' ADP 1101 B 1 HETATM 13 C C3' ADP . . . H 2 185.66 174.136 193.403 1 27.67 ? C3' ADP 1101 B 1 HETATM 14 O O3' ADP . . . H 2 185.968 175.139 194.377 1 36.96 ? O3' ADP 1101 B 1 HETATM 15 C C2' ADP . . . H 2 184.361 173.429 193.77 1 26.57 ? C2' ADP 1101 B 1 HETATM 16 O O2' ADP . . . H 2 184.326 172.937 195.098 1 41.78 ? O2' ADP 1101 B 1 HETATM 17 C C1' ADP . . . H 2 183.344 174.525 193.46 1 22.28 ? C1' ADP 1101 B 1 HETATM 18 N N9 ADP . . . H 2 181.975 174.006 193.266 1 24.17 ? N9 ADP 1101 B 1 HETATM 19 C C8 ADP . . . H 2 181.005 173.917 194.242 1 30.57 ? C8 ADP 1101 B 1 HETATM 20 N N7 ADP . . . H 2 179.868 173.428 193.817 1 30.4 ? N7 ADP 1101 B 1 HETATM 21 C C5 ADP . . . H 2 180.064 173.188 192.456 1 17.63 ? C5 ADP 1101 B 1 HETATM 22 C C6 ADP . . . H 2 179.245 172.682 191.422 1 26.42 ? C6 ADP 1101 B 1 HETATM 23 N N6 ADP . . . H 2 177.977 172.288 191.555 1 48.07 ? N6 ADP 1101 B 1 HETATM 24 N N1 ADP . . . H 2 179.787 172.529 190.17 1 32.31 ? N1 ADP 1101 B 1 HETATM 25 C C2 ADP . . . H 2 181.035 172.927 189.979 1 31.78 ? C2 ADP 1101 B 1 HETATM 26 N N3 ADP . . . H 2 181.929 173.414 190.874 1 25.56 ? N3 ADP 1101 B 1 HETATM 27 C C4 ADP . . . H 2 181.38 173.528 192.122 1 16.17 ? C4 ADP 1101 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 57 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #