data_8DUJ # _model_server_result.job_id iFqLJJLffIazyaaVY4e0PA _model_server_result.datetime_utc '2024-11-21 23:29:55' _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 8duj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":5103}' # _entry.id 8DUJ # _exptl.entry_id 8DUJ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 7 _entity.src_method nat _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 8DUJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DUJ _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 tridecameric _pdbx_struct_assembly.oligomeric_count 13 _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,Y,Z,AA,BA,CA _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 ? 7 P N N ? 7 T N N ? 7 X N N ? 7 BA 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 3 M CYS 3 1_555 A SG CYS 17 M CYS 17 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 3 M CYS 3 1_555 A SG CYS 17 M CYS 17 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 10 M CYS 10 1_555 A SG CYS 21 M CYS 21 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 10 M CYS 10 1_555 A SG CYS 21 M CYS 21 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 16 M CYS 16 1_555 A SG CYS 32 M CYS 32 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 A SG CYS 16 M CYS 16 1_555 A SG CYS 32 M CYS 32 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 2310 G CYS 2310 1_555 B SG CYS 2326 G CYS 2326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 4876 G CYS 4876 1_555 B SG CYS 4882 G CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 E SG CYS 2310 A CYS 2310 1_555 E SG CYS 2326 A CYS 2326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 E SG CYS 4876 A CYS 4876 1_555 E SG CYS 4882 A CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 H SG CYS 2310 D CYS 2310 1_555 H SG CYS 2326 D CYS 2326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 H SG CYS 4876 D CYS 4876 1_555 H SG CYS 4882 D CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 K SG CYS 36 J CYS 36 1_555 K SG CYS 65 J CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf14 K SG CYS 2310 J CYS 2310 1_555 K SG CYS 2326 J CYS 2326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 K SG CYS 4876 J CYS 4876 1_555 K SG CYS 4882 J CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 B OE1 GLU 3893 G GLU 3893 1_555 O CA CA . G CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc2 B OE2 GLU 3893 G GLU 3893 1_555 O CA CA . G CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc3 B OE1 GLU 3967 G GLU 3967 1_555 O CA CA . G CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc4 B OE2 GLU 3967 G GLU 3967 1_555 O CA CA . G CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc5 B SG CYS 4958 G CYS 4958 1_555 Q ZN ZN . G ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc6 B SG CYS 4961 G CYS 4961 1_555 Q ZN ZN . G ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc7 B NE2 HIS 4978 G HIS 4978 1_555 Q ZN ZN . G ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc8 B ND1 HIS 4983 G HIS 4983 1_555 Q ZN ZN . G ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc9 B O THR 5001 G THR 5001 1_555 O CA CA . G CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc10 E OE1 GLU 3967 A GLU 3967 1_555 S CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.105 ? metalc ? metalc11 E OE1 GLN 3970 A GLN 3970 1_555 S CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc12 E SG CYS 4958 A CYS 4958 1_555 U ZN ZN . A ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc13 E SG CYS 4961 A CYS 4961 1_555 U ZN ZN . A ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc14 E NE2 HIS 4978 A HIS 4978 1_555 U ZN ZN . A ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc15 E ND1 HIS 4983 A HIS 4983 1_555 U ZN ZN . A ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc16 E O THR 5001 A THR 5001 1_555 S CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc17 H OE1 GLU 3893 D GLU 3893 1_555 W CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.968 ? metalc ? metalc18 H OE2 GLU 3893 D GLU 3893 1_555 W CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc19 H OE1 GLU 3967 D GLU 3967 1_555 W CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc20 H OE2 GLU 3967 D GLU 3967 1_555 W CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc21 H SG CYS 4958 D CYS 4958 1_555 Y ZN ZN . D ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc22 H SG CYS 4961 D CYS 4961 1_555 Y ZN ZN . D ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc23 H NE2 HIS 4978 D HIS 4978 1_555 Y ZN ZN . D ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc24 H ND1 HIS 4983 D HIS 4983 1_555 Y ZN ZN . D ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc25 H O THR 5001 D THR 5001 1_555 W CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc26 K OE1 GLU 3893 J GLU 3893 1_555 AA CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? metalc ? metalc27 K OE1 GLU 3967 J GLU 3967 1_555 AA CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc28 K OE2 GLU 3967 J GLU 3967 1_555 AA CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc29 K OE1 GLN 3970 J GLN 3970 1_555 AA CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc30 K SG CYS 4958 J CYS 4958 1_555 CA ZN ZN . J ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc31 K SG CYS 4961 J CYS 4961 1_555 CA ZN ZN . J ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc32 K NE2 HIS 4978 J HIS 4978 1_555 CA ZN ZN . J ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc33 K ND1 HIS 4983 J HIS 4983 1_555 CA ZN ZN . J ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc34 K O THR 5001 J THR 5001 1_555 AA CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? # _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 8DUJ _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 N 5 CFF G 1 5101 5101 CFF CFF . O 6 CA G 1 5102 5201 CA CA . P 7 ATP G 1 5103 5301 ATP ATP . Q 8 ZN G 1 5104 5401 ZN ZN . R 5 CFF A 1 5101 5101 CFF CFF . S 6 CA A 1 5102 5201 CA CA . T 7 ATP A 1 5103 5301 ATP ATP . U 8 ZN A 1 5104 5401 ZN ZN . V 5 CFF D 1 5101 5101 CFF CFF . W 6 CA D 1 5102 5201 CA CA . X 7 ATP D 1 5103 5301 ATP ATP . Y 8 ZN D 1 5104 5401 ZN ZN . Z 5 CFF J 1 5101 5101 CFF CFF . AA 6 CA J 1 5102 5201 CA CA . BA 7 ATP J 1 5103 5301 ATP ATP . CA 8 ZN J 1 5104 5401 ZN ZN . # 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 . . . T 7 282.702 267.291 252.99 1 44.85 ? PG ATP 5103 A 1 HETATM 2 O O1G ATP . . . T 7 283.839 267.215 252.029 1 44.85 ? O1G ATP 5103 A 1 HETATM 3 O O2G ATP . . . T 7 282.836 268.425 254.012 1 44.85 ? O2G ATP 5103 A 1 HETATM 4 O O3G ATP . . . T 7 281.329 267.385 252.313 1 44.85 ? O3G ATP 5103 A 1 HETATM 5 P PB ATP . . . T 7 283.354 265.276 255.112 1 44.85 ? PB ATP 5103 A 1 HETATM 6 O O1B ATP . . . T 7 282.439 265.079 256.254 1 44.85 ? O1B ATP 5103 A 1 HETATM 7 O O2B ATP . . . T 7 284.612 266.095 255.404 1 44.85 ? O2B ATP 5103 A 1 HETATM 8 O O3B ATP . . . T 7 282.623 265.96 253.875 1 44.85 ? O3B ATP 5103 A 1 HETATM 9 P PA ATP . . . T 7 283.146 262.523 254.044 1 44.85 ? PA ATP 5103 A 1 HETATM 10 O O1A ATP . . . T 7 283.674 261.383 254.821 1 44.85 ? O1A ATP 5103 A 1 HETATM 11 O O2A ATP . . . T 7 283.315 262.405 252.529 1 44.85 ? O2A ATP 5103 A 1 HETATM 12 O O3A ATP . . . T 7 283.828 263.892 254.484 1 44.85 ? O3A ATP 5103 A 1 HETATM 13 O O5' ATP . . . T 7 281.618 262.774 254.357 1 44.85 ? O5' ATP 5103 A 1 HETATM 14 C C5' ATP . . . T 7 280.743 261.692 254.74 1 44.85 ? C5' ATP 5103 A 1 HETATM 15 C C4' ATP . . . T 7 280.754 260.649 253.651 1 44.85 ? C4' ATP 5103 A 1 HETATM 16 O O4' ATP . . . T 7 280.033 259.476 254.093 1 44.85 ? O4' ATP 5103 A 1 HETATM 17 C C3' ATP . . . T 7 280.114 261.078 252.33 1 44.85 ? C3' ATP 5103 A 1 HETATM 18 O O3' ATP . . . T 7 280.847 260.576 251.219 1 44.85 ? O3' ATP 5103 A 1 HETATM 19 C C2' ATP . . . T 7 278.716 260.462 252.414 1 44.85 ? C2' ATP 5103 A 1 HETATM 20 O O2' ATP . . . T 7 278.181 260.182 251.125 1 44.85 ? O2' ATP 5103 A 1 HETATM 21 C C1' ATP . . . T 7 279.01 259.166 253.168 1 44.85 ? C1' ATP 5103 A 1 HETATM 22 N N9 ATP . . . T 7 277.869 258.628 253.9 1 44.85 ? N9 ATP 5103 A 1 HETATM 23 C C8 ATP . . . T 7 277.276 257.405 253.72 1 44.85 ? C8 ATP 5103 A 1 HETATM 24 N N7 ATP . . . T 7 276.261 257.178 254.516 1 44.85 ? N7 ATP 5103 A 1 HETATM 25 C C5 ATP . . . T 7 276.178 258.333 255.279 1 44.85 ? C5 ATP 5103 A 1 HETATM 26 C C6 ATP . . . T 7 275.305 258.731 256.309 1 44.85 ? C6 ATP 5103 A 1 HETATM 27 N N6 ATP . . . T 7 274.307 257.972 256.774 1 44.85 ? N6 ATP 5103 A 1 HETATM 28 N N1 ATP . . . T 7 275.494 259.952 256.858 1 44.85 ? N1 ATP 5103 A 1 HETATM 29 C C2 ATP . . . T 7 276.489 260.716 256.398 1 44.85 ? C2 ATP 5103 A 1 HETATM 30 N N3 ATP . . . T 7 277.371 260.449 255.432 1 44.85 ? N3 ATP 5103 A 1 HETATM 31 C C4 ATP . . . T 7 277.162 259.237 254.909 1 44.85 ? C4 ATP 5103 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 136 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 31 #