data_8VJK # _model_server_result.job_id Zii4CdzxkV-mJTnghMy1FQ _model_server_result.datetime_utc '2024-11-08 02:48:11' _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 8vjk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":8003}' # _entry.id 8VJK # _exptl.entry_id 8VJK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _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 8VJK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VJK _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_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,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 ? 5 K N N ? 5 M N N ? 5 R N N ? 5 T N N ? 5 Y N N ? 5 AA N N ? 5 GA N N ? 5 IA 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 3171 A CYS 3171 1_555 A SG CYS 3241 A CYS 3241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 4874 A CYS 4874 1_555 A SG CYS 4880 A CYS 4880 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 F SG CYS 3171 B CYS 3171 1_555 F SG CYS 3241 B CYS 3241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 F SG CYS 4874 B CYS 4874 1_555 F SG CYS 4880 B CYS 4880 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 G SG CYS 3171 C CYS 3171 1_555 G SG CYS 3241 C CYS 3241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 G SG CYS 4874 C CYS 4874 1_555 G SG CYS 4880 C CYS 4880 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 H SG CYS 3171 D CYS 3171 1_555 H SG CYS 3241 D CYS 3241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf8 H SG CYS 4874 D CYS 4874 1_555 H SG CYS 4880 D CYS 4880 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A OE2 GLU 3896 A GLU 3896 1_555 L CA CA . A CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc2 A OE2 GLU 3970 A GLU 3970 1_555 L CA CA . A CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 A SG CYS 4956 A CYS 4956 1_555 I ZN ZN . A ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc4 A SG CYS 4959 A CYS 4959 1_555 I ZN ZN . A ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc5 A NE2 HIS 4976 A HIS 4976 1_555 I ZN ZN . A ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc6 A ND1 HIS 4981 A HIS 4981 1_555 I ZN ZN . A ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc7 A O THR 4999 A THR 4999 1_555 L CA CA . A CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc8 F OE2 GLU 3896 B GLU 3896 1_555 S CA CA . B CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc9 F OE2 GLU 3970 B GLU 3970 1_555 S CA CA . B CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc10 F SG CYS 4956 B CYS 4956 1_555 P ZN ZN . B ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc11 F SG CYS 4959 B CYS 4959 1_555 P ZN ZN . B ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc12 F NE2 HIS 4976 B HIS 4976 1_555 P ZN ZN . B ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc13 F ND1 HIS 4981 B HIS 4981 1_555 P ZN ZN . B ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc14 F O THR 4999 B THR 4999 1_555 S CA CA . B CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc15 G OE2 GLU 3896 C GLU 3896 1_555 Z CA CA . C CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc16 G OE2 GLU 3970 C GLU 3970 1_555 Z CA CA . C CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc17 G SG CYS 4956 C CYS 4956 1_555 W ZN ZN . C ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc18 G SG CYS 4959 C CYS 4959 1_555 W ZN ZN . C ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc19 G NE2 HIS 4976 C HIS 4976 1_555 W ZN ZN . C ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc20 G ND1 HIS 4981 C HIS 4981 1_555 W ZN ZN . C ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc21 G O THR 4999 C THR 4999 1_555 Z CA CA . C CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc22 H OE2 GLU 3896 D GLU 3896 1_555 HA CA CA . D CA 5105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc23 H OE2 GLU 3970 D GLU 3970 1_555 HA CA CA . D CA 5105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc24 H SG CYS 4956 D CYS 4956 1_555 EA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc25 H SG CYS 4959 D CYS 4959 1_555 EA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc26 H NE2 HIS 4976 D HIS 4976 1_555 EA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc27 H ND1 HIS 4981 D HIS 4981 1_555 EA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc28 H O THR 4999 D THR 4999 1_555 HA CA CA . D CA 5105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _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 8VJK _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 ZN A 1 8001 8001 ZN ZN . J 4 CFF A 1 8002 8002 CFF CFF . K 5 ATP A 1 8003 8003 ATP ATP . L 6 CA A 1 8004 8004 CA CA . M 5 ATP A 1 8005 8005 ATP ATP . N 7 PCW A 1 8006 8007 PCW PCW . O 7 PCW A 1 8007 8008 PCW PCW . P 3 ZN B 1 8001 8001 ZN ZN . Q 4 CFF B 1 8002 8002 CFF CFF . R 5 ATP B 1 8003 8003 ATP ATP . S 6 CA B 1 8004 8004 CA CA . T 5 ATP B 1 8005 8005 ATP ATP . U 7 PCW B 1 8006 8007 PCW PCW . V 7 PCW B 1 8007 8008 PCW PCW . W 3 ZN C 1 8001 8001 ZN ZN . X 4 CFF C 1 8002 8002 CFF CFF . Y 5 ATP C 1 8003 8003 ATP ATP . Z 6 CA C 1 8004 8004 CA CA . AA 5 ATP C 1 8005 8005 ATP ATP . BA 7 PCW C 1 8006 8007 PCW PCW . CA 7 PCW C 1 8007 8008 PCW PCW . DA 7 PCW D 1 5101 8008 PCW PCW . EA 3 ZN D 1 5102 8001 ZN ZN . FA 4 CFF D 1 5103 8002 CFF CFF . GA 5 ATP D 1 5104 8003 ATP ATP . HA 6 CA D 1 5105 8004 CA CA . IA 5 ATP D 1 5106 8005 ATP ATP . JA 7 PCW D 1 5107 8007 PCW PCW . # 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 . . . Y 5 228.117 234.231 169.837 1 87.6 ? PG ATP 8003 C 1 HETATM 2 O O1G ATP . . . Y 5 227.076 233.154 169.662 1 87.6 ? O1G ATP 8003 C 1 HETATM 3 O O2G ATP . . . Y 5 229.481 233.806 169.356 1 87.6 ? O2G ATP 8003 C 1 HETATM 4 O O3G ATP . . . Y 5 227.683 235.556 169.264 1 87.6 ? O3G ATP 8003 C 1 HETATM 5 P PB ATP . . . Y 5 227.338 235.114 172.54 1 87.6 ? PB ATP 8003 C 1 HETATM 6 O O1B ATP . . . Y 5 228.199 235.876 173.491 1 87.6 ? O1B ATP 8003 C 1 HETATM 7 O O2B ATP . . . Y 5 226.193 235.798 171.869 1 87.6 ? O2B ATP 8003 C 1 HETATM 8 O O3B ATP . . . Y 5 228.276 234.455 171.425 1 87.6 ? O3B ATP 8003 C 1 HETATM 9 P PA ATP . . . Y 5 225.893 232.573 172.795 1 87.6 ? PA ATP 8003 C 1 HETATM 10 O O1A ATP . . . Y 5 226.79 231.489 172.295 1 87.6 ? O1A ATP 8003 C 1 HETATM 11 O O2A ATP . . . Y 5 224.826 233.082 171.884 1 87.6 ? O2A ATP 8003 C 1 HETATM 12 O O3A ATP . . . Y 5 226.795 233.805 173.281 1 87.6 ? O3A ATP 8003 C 1 HETATM 13 O O5' ATP . . . Y 5 225.235 232.127 174.186 1 87.6 ? O5' ATP 8003 C 1 HETATM 14 C C5' ATP . . . Y 5 225.761 230.96 174.863 1 87.6 ? C5' ATP 8003 C 1 HETATM 15 C C4' ATP . . . Y 5 224.665 229.934 174.999 1 87.6 ? C4' ATP 8003 C 1 HETATM 16 O O4' ATP . . . Y 5 225.214 228.735 175.604 1 87.6 ? O4' ATP 8003 C 1 HETATM 17 C C3' ATP . . . Y 5 223.475 230.336 175.882 1 87.6 ? C3' ATP 8003 C 1 HETATM 18 O O3' ATP . . . Y 5 222.257 229.844 175.339 1 87.6 ? O3' ATP 8003 C 1 HETATM 19 C C2' ATP . . . Y 5 223.817 229.679 177.221 1 87.6 ? C2' ATP 8003 C 1 HETATM 20 O O2' ATP . . . Y 5 222.688 229.434 178.03 1 87.6 ? O2' ATP 8003 C 1 HETATM 21 C C1' ATP . . . Y 5 224.457 228.383 176.737 1 87.6 ? C1' ATP 8003 C 1 HETATM 22 N N9 ATP . . . Y 5 225.338 227.743 177.707 1 87.6 ? N9 ATP 8003 C 1 HETATM 23 C C8 ATP . . . Y 5 225.161 226.513 178.28 1 87.6 ? C8 ATP 8003 C 1 HETATM 24 N N7 ATP . . . Y 5 226.118 226.207 179.123 1 87.6 ? N7 ATP 8003 C 1 HETATM 25 C C5 ATP . . . Y 5 226.971 227.302 179.099 1 87.6 ? C5 ATP 8003 C 1 HETATM 26 C C6 ATP . . . Y 5 228.17 227.586 179.777 1 87.6 ? C6 ATP 8003 C 1 HETATM 27 N N6 ATP . . . Y 5 228.738 226.758 180.647 1 87.6 ? N6 ATP 8003 C 1 HETATM 28 N N1 ATP . . . Y 5 228.763 228.775 179.52 1 87.6 ? N1 ATP 8003 C 1 HETATM 29 C C2 ATP . . . Y 5 228.183 229.604 178.643 1 87.6 ? C2 ATP 8003 C 1 HETATM 30 N N3 ATP . . . Y 5 227.06 229.442 177.95 1 87.6 ? N3 ATP 8003 C 1 HETATM 31 C C4 ATP . . . Y 5 226.497 228.256 178.227 1 87.6 ? C4 ATP 8003 C 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 149 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #