data_8DVE # _model_server_result.job_id a6PkRazbYC8LrIX-VFkP3A _model_server_result.datetime_utc '2025-03-05 03:21:49' _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 8dve # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":5103}' # _entry.id 8DVE # _exptl.entry_id 8DVE _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 6 _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 8DVE _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DVE _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 dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 _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 ? 6 O N N ? 6 S N N ? 6 W N N ? 6 AA 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 4876 D CYS 4876 1_555 A SG CYS 4882 D CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 D SG CYS 4876 A CYS 4876 1_555 D SG CYS 4882 A CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 G SG CYS 4876 G CYS 4876 1_555 G SG CYS 4882 G CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 J SG CYS 4876 J CYS 4876 1_555 J SG CYS 4882 J CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A OE1 GLU 3893 D GLU 3893 1_555 N CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc2 A OE2 GLU 3893 D GLU 3893 1_555 N CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc3 A OE1 GLU 3967 D GLU 3967 1_555 N CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc4 A OE2 GLU 3967 D GLU 3967 1_555 N CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc5 A SG CYS 4961 D CYS 4961 1_555 P ZN ZN . D ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc6 A NE2 HIS 4978 D HIS 4978 1_555 P ZN ZN . D ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc7 A ND1 HIS 4983 D HIS 4983 1_555 P ZN ZN . D ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc8 A O THR 5001 D THR 5001 1_555 N CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc9 D OE1 GLU 3893 A GLU 3893 1_555 R CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc10 D OE2 GLU 3893 A GLU 3893 1_555 R CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc11 D OE1 GLU 3967 A GLU 3967 1_555 R CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc12 D OE2 GLU 3967 A GLU 3967 1_555 R CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc13 D SG CYS 4958 A CYS 4958 1_555 T ZN ZN . A ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc14 D SG CYS 4961 A CYS 4961 1_555 T ZN ZN . A ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc15 D NE2 HIS 4978 A HIS 4978 1_555 T ZN ZN . A ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc16 D ND1 HIS 4983 A HIS 4983 1_555 T ZN ZN . A ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc17 D O THR 5001 A THR 5001 1_555 R CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc18 D OG1 THR 5001 A THR 5001 1_555 R CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc19 G OE1 GLU 3893 G GLU 3893 1_555 V CA CA . G CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc20 G OE2 GLU 3893 G GLU 3893 1_555 V CA CA . G CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc21 G OE1 GLU 3967 G GLU 3967 1_555 V CA CA . G CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc22 G OE2 GLU 3967 G GLU 3967 1_555 V CA CA . G CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc23 G SG CYS 4958 G CYS 4958 1_555 X ZN ZN . G ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc24 G SG CYS 4961 G CYS 4961 1_555 X ZN ZN . G ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc25 G NE2 HIS 4978 G HIS 4978 1_555 X ZN ZN . G ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc26 G ND1 HIS 4983 G HIS 4983 1_555 X ZN ZN . G ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc27 G O THR 5001 G THR 5001 1_555 V CA CA . G CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc28 J OE1 GLU 3893 J GLU 3893 1_555 Z CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc29 J OE2 GLU 3893 J GLU 3893 1_555 Z CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc30 J OE1 GLU 3967 J GLU 3967 1_555 Z CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc31 J OE2 GLU 3967 J GLU 3967 1_555 Z CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc32 J OE1 GLN 3970 J GLN 3970 1_555 Z CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc33 J SG CYS 4961 J CYS 4961 1_555 BA ZN ZN . J ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc34 J NE2 HIS 4978 J HIS 4978 1_555 BA ZN ZN . J ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc35 J ND1 HIS 4983 J HIS 4983 1_555 BA ZN ZN . J ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc36 J O THR 5001 J THR 5001 1_555 Z CA CA . J CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc37 J SG CYS 5027 J CYS 5027 1_555 BA ZN ZN . J ZN 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? # _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 8DVE _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 M 4 CFF D 1 5101 5101 CFF CFF . N 5 CA D 1 5102 5201 CA CA . O 6 ATP D 1 5103 5301 ATP ATP . P 7 ZN D 1 5104 5401 ZN ZN . Q 4 CFF A 1 5101 5101 CFF CFF . R 5 CA A 1 5102 5201 CA CA . S 6 ATP A 1 5103 5301 ATP ATP . T 7 ZN A 1 5104 5401 ZN ZN . U 4 CFF G 1 5101 5101 CFF CFF . V 5 CA G 1 5102 5201 CA CA . W 6 ATP G 1 5103 5301 ATP ATP . X 7 ZN G 1 5104 5401 ZN ZN . Y 4 CFF J 1 5101 5101 CFF CFF . Z 5 CA J 1 5102 5201 CA CA . AA 6 ATP J 1 5103 5301 ATP ATP . BA 7 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 . . . S 6 196.999 226.008 265.117 1 101.76 ? PG ATP 5103 A 1 HETATM 2 O O1G ATP . . . S 6 198.288 225.65 265.775 1 101.76 ? O1G ATP 5103 A 1 HETATM 3 O O2G ATP . . . S 6 196.434 227.36 265.564 1 101.76 ? O2G ATP 5103 A 1 HETATM 4 O O3G ATP . . . S 6 195.914 224.935 265.268 1 101.76 ? O3G ATP 5103 A 1 HETATM 5 P PB ATP . . . S 6 198.154 225.637 262.375 1 101.76 ? PB ATP 5103 A 1 HETATM 6 O O1B ATP . . . S 6 197.587 224.463 261.681 1 101.76 ? O1B ATP 5103 A 1 HETATM 7 O O2B ATP . . . S 6 199.543 225.444 262.983 1 101.76 ? O2B ATP 5103 A 1 HETATM 8 O O3B ATP . . . S 6 197.197 226.157 263.536 1 101.76 ? O3B ATP 5103 A 1 HETATM 9 P PA ATP . . . S 6 198.603 228.448 261.557 1 101.76 ? PA ATP 5103 A 1 HETATM 10 O O1A ATP . . . S 6 199.277 228.73 262.841 1 101.76 ? O1A ATP 5103 A 1 HETATM 11 O O2A ATP . . . S 6 197.326 229.247 261.298 1 101.76 ? O2A ATP 5103 A 1 HETATM 12 O O3A ATP . . . S 6 198.23 226.906 261.417 1 101.76 ? O3A ATP 5103 A 1 HETATM 13 O O5' ATP . . . S 6 199.589 228.671 260.344 1 101.76 ? O5' ATP 5103 A 1 HETATM 14 C C5' ATP . . . S 6 200.685 227.766 260.096 1 101.76 ? C5' ATP 5103 A 1 HETATM 15 C C4' ATP . . . S 6 201.361 228.146 258.802 1 101.76 ? C4' ATP 5103 A 1 HETATM 16 O O4' ATP . . . S 6 201.497 229.58 258.729 1 101.76 ? O4' ATP 5103 A 1 HETATM 17 C C3' ATP . . . S 6 202.779 227.619 258.635 1 101.76 ? C3' ATP 5103 A 1 HETATM 18 O O3' ATP . . . S 6 202.772 226.289 258.128 1 101.76 ? O3' ATP 5103 A 1 HETATM 19 C C2' ATP . . . S 6 203.379 228.606 257.63 1 101.76 ? C2' ATP 5103 A 1 HETATM 20 O O2' ATP . . . S 6 203.107 228.224 256.286 1 101.76 ? O2' ATP 5103 A 1 HETATM 21 C C1' ATP . . . S 6 202.653 229.914 257.977 1 101.76 ? C1' ATP 5103 A 1 HETATM 22 N N9 ATP . . . S 6 203.458 230.863 258.743 1 101.76 ? N9 ATP 5103 A 1 HETATM 23 C C8 ATP . . . S 6 204.336 231.784 258.233 1 101.76 ? C8 ATP 5103 A 1 HETATM 24 N N7 ATP . . . S 6 204.933 232.517 259.141 1 101.76 ? N7 ATP 5103 A 1 HETATM 25 C C5 ATP . . . S 6 204.412 232.045 260.337 1 101.76 ? C5 ATP 5103 A 1 HETATM 26 C C6 ATP . . . S 6 204.638 232.405 261.679 1 101.76 ? C6 ATP 5103 A 1 HETATM 27 N N6 ATP . . . S 6 205.485 233.368 262.059 1 101.76 ? N6 ATP 5103 A 1 HETATM 28 N N1 ATP . . . S 6 203.956 231.735 262.634 1 101.76 ? N1 ATP 5103 A 1 HETATM 29 C C2 ATP . . . S 6 203.109 230.772 262.263 1 101.76 ? C2 ATP 5103 A 1 HETATM 30 N N3 ATP . . . S 6 202.815 230.346 261.033 1 101.76 ? N3 ATP 5103 A 1 HETATM 31 C C4 ATP . . . S 6 203.502 231.025 260.108 1 101.76 ? C4 ATP 5103 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 537 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #