data_8XVB # _model_server_result.job_id 7cDWnlQ5UGi-JKE6Z9jQwg _model_server_result.datetime_utc '2024-12-22 08:53:28' _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 8xvb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":401}' # _entry.id 8XVB # _exptl.entry_id 8XVB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 8 _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 8XVB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XVB _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 decameric _pdbx_struct_assembly.oligomeric_count 10 _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 _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 ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 Q N N ? 4 R 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 hydrog 'DA-DT PAIR' hydrog1 A N3 DA 6 I DA 6 1_555 J N3 DT 20 J DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N1 DA 7 I DA 7 1_555 J N3 DT 18 J DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N6 DA 7 I DA 7 1_555 J O4 DT 18 J DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DA 10 I DA 10 1_555 J N3 DT 15 J DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 DA 10 I DA 10 1_555 J O4 DT 15 J DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DA 11 I DA 11 1_555 J N3 DT 14 J DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 DA 11 I DA 11 1_555 J O4 DT 14 J DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 DA 12 I DA 12 1_555 J N3 DT 13 J DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N6 DA 12 I DA 12 1_555 J O4 DT 13 J DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DA 13 I DA 13 1_555 J N3 DT 12 J DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N6 DA 13 I DA 13 1_555 J O4 DT 12 J DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 DA 15 I DA 15 1_555 J N3 DT 10 J DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N6 DA 15 I DA 15 1_555 J O4 DT 10 J DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 DA 16 I DA 16 1_555 J N3 DT 9 J DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N6 DA 16 I DA 16 1_555 J O4 DT 9 J DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog16 A N1 DA 17 I DA 17 1_555 J N3 DT 9 J DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 DA 18 I DA 18 1_555 J N3 DT 7 J DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N6 DA 18 I DA 18 1_555 J O4 DT 7 J DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 DA 19 I DA 19 1_555 J N3 DT 6 J DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N6 DA 19 I DA 19 1_555 J O4 DT 6 J DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N1 DA 20 I DA 20 1_555 J N3 DT 5 J DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N6 DA 20 I DA 20 1_555 J O4 DT 5 J DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 DA 21 I DA 21 1_555 J N3 DT 4 J DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N6 DA 21 I DA 21 1_555 J O4 DT 4 J DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N1 DA 22 I DA 22 1_555 J N3 DT 3 J DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N6 DA 22 I DA 22 1_555 J O4 DT 3 J DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N1 DA 23 I DA 23 1_555 J N3 DT 2 J DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N6 DA 23 I DA 23 1_555 J O4 DT 2 J DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N1 DA 24 I DA 24 1_555 J N3 DT 1 J DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N6 DA 24 I DA 24 1_555 J O4 DT 1 J DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 8XVB _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 K 4 ATP A 1 401 401 ATP ATP . L 4 ATP B 1 401 401 ATP ATP . M 4 ATP C 1 401 401 ATP ATP . N 4 ATP D 1 401 401 ATP ATP . O 4 ATP E 1 401 401 ATP ATP . P 4 ATP F 1 401 401 ATP ATP . Q 4 ATP G 1 401 401 ATP ATP . R 4 ATP H 1 401 401 ATP ATP . # 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 PG ATP . . . Q 4 118.431 112.885 106.042 1 28.46 ? PG ATP 401 G 1 HETATM 2 O O1G ATP . . . Q 4 117.901 114.186 106.54 1 28.46 ? O1G ATP 401 G 1 HETATM 3 O O2G ATP . . . Q 4 118.909 112.931 104.587 1 28.46 ? O2G ATP 401 G 1 HETATM 4 O O3G ATP . . . Q 4 119.545 112.301 106.918 1 28.46 ? O3G ATP 401 G 1 HETATM 5 P PB ATP . . . Q 4 116.643 110.684 105.089 1 28.46 ? PB ATP 401 G 1 HETATM 6 O O1B ATP . . . Q 4 116.425 111.22 103.732 1 28.46 ? O1B ATP 401 G 1 HETATM 7 O O2B ATP . . . Q 4 117.514 109.432 105.169 1 28.46 ? O2B ATP 401 G 1 HETATM 8 O O3B ATP . . . Q 4 117.286 111.771 106.052 1 28.46 ? O3B ATP 401 G 1 HETATM 9 P PA ATP . . . Q 4 114.436 109.056 106.196 1 28.46 ? PA ATP 401 G 1 HETATM 10 O O1A ATP . . . Q 4 115.251 108.092 106.962 1 28.46 ? O1A ATP 401 G 1 HETATM 11 O O2A ATP . . . Q 4 113.859 108.519 104.887 1 28.46 ? O2A ATP 401 G 1 HETATM 12 O O3A ATP . . . Q 4 115.275 110.357 105.835 1 28.46 ? O3A ATP 401 G 1 HETATM 13 O O5' ATP . . . Q 4 113.251 109.608 107.081 1 28.46 ? O5' ATP 401 G 1 HETATM 14 C C5' ATP . . . Q 4 112.389 110.664 106.609 1 28.46 ? C5' ATP 401 G 1 HETATM 15 C C4' ATP . . . Q 4 111.055 110.084 106.209 1 28.46 ? C4' ATP 401 G 1 HETATM 16 O O4' ATP . . . Q 4 111.208 108.685 105.876 1 28.46 ? O4' ATP 401 G 1 HETATM 17 C C3' ATP . . . Q 4 109.96 110.155 107.273 1 28.46 ? C3' ATP 401 G 1 HETATM 18 O O3' ATP . . . Q 4 108.696 110.444 106.688 1 28.46 ? O3' ATP 401 G 1 HETATM 19 C C2' ATP . . . Q 4 109.991 108.754 107.887 1 28.46 ? C2' ATP 401 G 1 HETATM 20 O O2' ATP . . . Q 4 108.724 108.38 108.416 1 28.46 ? O2' ATP 401 G 1 HETATM 21 C C1' ATP . . . Q 4 110.333 107.904 106.665 1 28.46 ? C1' ATP 401 G 1 HETATM 22 N N9 ATP . . . Q 4 110.999 106.645 106.981 1 28.46 ? N9 ATP 401 G 1 HETATM 23 C C8 ATP . . . Q 4 112.345 106.388 106.938 1 28.46 ? C8 ATP 401 G 1 HETATM 24 N N7 ATP . . . Q 4 112.666 105.162 107.272 1 28.46 ? N7 ATP 401 G 1 HETATM 25 C C5 ATP . . . Q 4 111.446 104.569 107.558 1 28.46 ? C5 ATP 401 G 1 HETATM 26 C C6 ATP . . . Q 4 111.094 103.271 107.974 1 28.46 ? C6 ATP 401 G 1 HETATM 27 N N6 ATP . . . Q 4 111.979 102.292 108.186 1 28.46 ? N6 ATP 401 G 1 HETATM 28 N N1 ATP . . . Q 4 109.783 103.007 108.17 1 28.46 ? N1 ATP 401 G 1 HETATM 29 C C2 ATP . . . Q 4 108.894 103.98 107.96 1 28.46 ? C2 ATP 401 G 1 HETATM 30 N N3 ATP . . . Q 4 109.106 105.238 107.567 1 28.46 ? N3 ATP 401 G 1 HETATM 31 C C4 ATP . . . Q 4 110.409 105.472 107.382 1 28.46 ? C4 ATP 401 G 1 # _model_server_stats.io_time_ms 130 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #