data_9E1D # _model_server_result.job_id dtvhxuxjka59dxLAD-60UQ _model_server_result.datetime_utc '2025-01-02 17:17:05' _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 9e1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":5301}' # _entry.id 9E1D # _exptl.entry_id 9E1D _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 9E1D _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9E1D _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_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 _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 ? _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 I N N ? 3 M N N ? 3 Q N N ? 3 U 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 disulf ? disulf1 A SG CYS 2233 A CYS 2233 1_555 A SG CYS 2237 A CYS 2237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? disulf ? disulf2 A SG CYS 2702 A CYS 2702 1_555 A SG CYS 2704 A CYS 2704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 3170 A CYS 3170 1_555 A SG CYS 3240 A CYS 3240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 4876 A CYS 4876 1_555 A SG CYS 4882 A CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 F SG CYS 2233 B CYS 2233 1_555 F SG CYS 2237 B CYS 2237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? disulf ? disulf6 F SG CYS 2702 B CYS 2702 1_555 F SG CYS 2704 B CYS 2704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 F SG CYS 3170 B CYS 3170 1_555 F SG CYS 3240 B CYS 3240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 F SG CYS 4876 B CYS 4876 1_555 F SG CYS 4882 B CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 G SG CYS 2233 D CYS 2233 1_555 G SG CYS 2237 D CYS 2237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? disulf ? disulf10 G SG CYS 2702 D CYS 2702 1_555 G SG CYS 2704 D CYS 2704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 G SG CYS 3170 D CYS 3170 1_555 G SG CYS 3240 D CYS 3240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 G SG CYS 4876 D CYS 4876 1_555 G SG CYS 4882 D CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 H SG CYS 2233 C CYS 2233 1_555 H SG CYS 2237 C CYS 2237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? disulf ? disulf14 H SG CYS 2702 C CYS 2702 1_555 H SG CYS 2704 C CYS 2704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 H SG CYS 3170 C CYS 3170 1_555 H SG CYS 3240 C CYS 3240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf16 H SG CYS 4876 C CYS 4876 1_555 H SG CYS 4882 C CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A OE1 GLU 3893 A GLU 3893 1_555 J CA CA . A CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc2 A OE2 GLU 3893 A GLU 3893 1_555 J CA CA . A CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc3 A OE1 GLU 3967 A GLU 3967 1_555 J CA CA . A CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc4 A SG CYS 4958 A CYS 4958 1_555 K ZN ZN . A ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc5 A SG CYS 4961 A CYS 4961 1_555 K ZN ZN . A ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc6 A NE2 HIS 4978 A HIS 4978 1_555 K ZN ZN . A ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc7 A ND1 HIS 4983 A HIS 4983 1_555 K ZN ZN . A ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc8 A O THR 5001 A THR 5001 1_555 J CA CA . A CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc9 F OE1 GLU 3893 B GLU 3893 1_555 N CA CA . B CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc10 F OE2 GLU 3893 B GLU 3893 1_555 N CA CA . B CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc11 F OE1 GLU 3967 B GLU 3967 1_555 N CA CA . B CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc12 F SG CYS 4958 B CYS 4958 1_555 O ZN ZN . B ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc13 F SG CYS 4961 B CYS 4961 1_555 O ZN ZN . B ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc14 F NE2 HIS 4978 B HIS 4978 1_555 O ZN ZN . B ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc15 F ND1 HIS 4983 B HIS 4983 1_555 O ZN ZN . B ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc16 F O THR 5001 B THR 5001 1_555 N CA CA . B CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc17 G OE1 GLU 3893 D GLU 3893 1_555 R CA CA . D CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc18 G OE2 GLU 3893 D GLU 3893 1_555 R CA CA . D CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc19 G OE1 GLU 3967 D GLU 3967 1_555 R CA CA . D CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc20 G SG CYS 4958 D CYS 4958 1_555 S ZN ZN . D ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc21 G SG CYS 4961 D CYS 4961 1_555 S ZN ZN . D ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc22 G NE2 HIS 4978 D HIS 4978 1_555 S ZN ZN . D ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc23 G ND1 HIS 4983 D HIS 4983 1_555 S ZN ZN . D ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc24 G O THR 5001 D THR 5001 1_555 R CA CA . D CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc25 H OE1 GLU 3893 C GLU 3893 1_555 V CA CA . C CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc26 H OE2 GLU 3893 C GLU 3893 1_555 V CA CA . C CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc27 H OE1 GLU 3967 C GLU 3967 1_555 V CA CA . C CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc28 H SG CYS 4958 C CYS 4958 1_555 W ZN ZN . C ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc29 H SG CYS 4961 C CYS 4961 1_555 W ZN ZN . C ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc30 H NE2 HIS 4978 C HIS 4978 1_555 W ZN ZN . C ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc31 H ND1 HIS 4983 C HIS 4983 1_555 W ZN ZN . C ZN 5303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc32 H O THR 5001 C THR 5001 1_555 V CA CA . C CA 5302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? # _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 95 n n PG O2G ATP sing 96 n n PG O3G ATP sing 97 n n PG O3B ATP sing 98 n n O2G HOG2 ATP sing 99 n n O3G HOG3 ATP sing 100 n n PB O1B ATP doub 101 n n PB O2B ATP sing 102 n n PB O3B ATP sing 103 n n PB O3A ATP sing 104 n n O2B HOB2 ATP sing 105 n n PA O1A ATP doub 106 n n PA O2A ATP sing 107 n n PA O3A ATP sing 108 n n PA O5' ATP sing 109 n n O2A HOA2 ATP sing 110 n n O5' C5' ATP sing 111 n n C5' C4' ATP sing 112 n n C5' "H5'1" ATP sing 113 n n C5' "H5'2" ATP sing 114 n n C4' O4' ATP sing 115 n n C4' C3' ATP sing 116 n n C4' H4' ATP sing 117 n n O4' C1' ATP sing 118 n n C3' O3' ATP sing 119 n n C3' C2' ATP sing 120 n n C3' H3' ATP sing 121 n n O3' HO3' ATP sing 122 n n C2' O2' ATP sing 123 n n C2' C1' ATP sing 124 n n C2' H2' ATP sing 125 n n O2' HO2' ATP sing 126 n n C1' N9 ATP sing 127 n n C1' H1' ATP sing 128 n n N9 C8 ATP sing 129 n y N9 C4 ATP sing 130 n y C8 N7 ATP doub 131 n y C8 H8 ATP sing 132 n n N7 C5 ATP sing 133 n y C5 C6 ATP sing 134 n y C5 C4 ATP doub 135 n y C6 N6 ATP sing 136 n n C6 N1 ATP doub 137 n y N6 HN61 ATP sing 138 n n N6 HN62 ATP sing 139 n n N1 C2 ATP sing 140 n y C2 N3 ATP doub 141 n y C2 H2 ATP sing 142 n n N3 C4 ATP sing 143 n y # _atom_sites.entry_id 9E1D _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 I 3 ATP A 1 5301 5301 ATP ATP . J 4 CA A 1 5302 5302 CA CA . K 5 ZN A 1 5303 5303 ZN ZN . L 6 A1BD3 A 1 5304 5304 A1BD3 LIG . M 3 ATP B 1 5301 5301 ATP ATP . N 4 CA B 1 5302 5302 CA CA . O 5 ZN B 1 5303 5303 ZN ZN . P 6 A1BD3 B 1 5304 5304 A1BD3 LIG . Q 3 ATP D 1 5301 5301 ATP ATP . R 4 CA D 1 5302 5302 CA CA . S 5 ZN D 1 5303 5303 ZN ZN . T 6 A1BD3 D 1 5304 5304 A1BD3 LIG . U 3 ATP C 1 5301 5301 ATP ATP . V 4 CA C 1 5302 5302 CA CA . W 5 ZN C 1 5303 5303 ZN ZN . X 6 A1BD3 C 1 5304 5304 A1BD3 LIG . # 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 . . . U 3 227.461 192.69 259.313 1 86.33 ? PG ATP 5301 C 1 HETATM 2 O O1G ATP . . . U 3 226.057 193.19 259.356 1 86.33 ? O1G ATP 5301 C 1 HETATM 3 O O2G ATP . . . U 3 228.499 193.741 259.724 1 86.33 ? O2G ATP 5301 C 1 HETATM 4 O O3G ATP . . . U 3 227.687 191.414 260.131 1 86.33 ? O3G ATP 5301 C 1 HETATM 5 P PB ATP . . . U 3 228.002 192.947 256.38 1 86.33 ? PB ATP 5301 C 1 HETATM 6 O O1B ATP . . . U 3 229.358 192.781 255.818 1 86.33 ? O1B ATP 5301 C 1 HETATM 7 O O2B ATP . . . U 3 226.857 192.404 255.525 1 86.33 ? O2B ATP 5301 C 1 HETATM 8 O O3B ATP . . . U 3 227.868 192.288 257.82 1 86.33 ? O3B ATP 5301 C 1 HETATM 9 P PA ATP . . . U 3 226.579 195.534 256.255 1 86.33 ? PA ATP 5301 C 1 HETATM 10 O O1A ATP . . . U 3 227.074 196.918 256.403 1 86.33 ? O1A ATP 5301 C 1 HETATM 11 O O2A ATP . . . U 3 225.297 195.21 257.023 1 86.33 ? O2A ATP 5301 C 1 HETATM 12 O O3A ATP . . . U 3 227.67 194.471 256.699 1 86.33 ? O3A ATP 5301 C 1 HETATM 13 O O5' ATP . . . U 3 226.356 195.173 254.734 1 86.33 ? O5' ATP 5301 C 1 HETATM 14 C C5' ATP . . . U 3 226.817 196.045 253.683 1 86.33 ? C5' ATP 5301 C 1 HETATM 15 C C4' ATP . . . U 3 225.7 196.983 253.313 1 86.33 ? C4' ATP 5301 C 1 HETATM 16 O O4' ATP . . . U 3 226.3 198.25 253.001 1 86.33 ? O4' ATP 5301 C 1 HETATM 17 C C3' ATP . . . U 3 225.088 196.605 251.976 1 86.33 ? C3' ATP 5301 C 1 HETATM 18 O O3' ATP . . . U 3 223.998 195.744 252.278 1 86.33 ? O3' ATP 5301 C 1 HETATM 19 C C2' ATP . . . U 3 224.465 197.931 251.539 1 86.33 ? C2' ATP 5301 C 1 HETATM 20 O O2' ATP . . . U 3 223.288 198.087 252.318 1 86.33 ? O2' ATP 5301 C 1 HETATM 21 C C1' ATP . . . U 3 225.446 198.959 252.121 1 86.33 ? C1' ATP 5301 C 1 HETATM 22 N N9 ATP . . . U 3 226.292 199.531 251.082 1 86.33 ? N9 ATP 5301 C 1 HETATM 23 C C8 ATP . . . U 3 226.124 200.74 250.461 1 86.33 ? C8 ATP 5301 C 1 HETATM 24 N N7 ATP . . . U 3 227.032 201.007 249.555 1 86.33 ? N7 ATP 5301 C 1 HETATM 25 C C5 ATP . . . U 3 227.858 199.894 249.581 1 86.33 ? C5 ATP 5301 C 1 HETATM 26 C C6 ATP . . . U 3 229.015 199.552 248.855 1 86.33 ? C6 ATP 5301 C 1 HETATM 27 N N6 ATP . . . U 3 229.563 200.335 247.92 1 86.33 ? N6 ATP 5301 C 1 HETATM 28 N N1 ATP . . . U 3 229.598 198.363 249.125 1 86.33 ? N1 ATP 5301 C 1 HETATM 29 C C2 ATP . . . U 3 229.054 197.578 250.057 1 86.33 ? C2 ATP 5301 C 1 HETATM 30 N N3 ATP . . . U 3 227.969 197.793 250.804 1 86.33 ? N3 ATP 5301 C 1 HETATM 31 C C4 ATP . . . U 3 227.413 198.974 250.518 1 86.33 ? C4 ATP 5301 C 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 500 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #