data_8C4C # _model_server_result.job_id NId-k1nGlaUxtUtQUi75aw _model_server_result.datetime_utc '2025-09-05 07:33:00' _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 8c4c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":802}' # _entry.id 8C4C # _exptl.entry_id 8C4C _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 8C4C _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8C4C _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 12-meric _pdbx_struct_assembly.oligomeric_count 12 _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 ? 3 M N N ? 3 Q N N ? 3 S N N ? 3 W N N ? 3 Z N N ? 3 CA N N ? 3 FA N N ? 3 JA 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 covale ? covale1 A C GLU 74 A GLU 72 1_555 A N HIC 75 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C HIC 75 A HIC 73 1_555 A N GLY 76 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C GLU 74 B GLU 72 1_555 B N HIC 75 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 B C HIC 75 B HIC 73 1_555 B N GLY 76 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 C C GLU 74 C GLU 72 1_555 C N HIC 75 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 C C HIC 75 C HIC 73 1_555 C N GLY 76 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 D C GLU 74 D GLU 72 1_555 D N HIC 75 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 D C HIC 75 D HIC 73 1_555 D N GLY 76 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 E C GLU 74 E GLU 72 1_555 E N HIC 75 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 E C HIC 75 E HIC 73 1_555 E N GLY 76 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 F C GLU 74 F GLU 72 1_555 F N HIC 75 F HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 F C HIC 75 F HIC 73 1_555 F N GLY 76 F GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale13 G C GLU 74 G GLU 72 1_555 G N HIC 75 G HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 G C HIC 75 G HIC 73 1_555 G N GLY 76 G GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 H C GLU 74 H GLU 72 1_555 H N HIC 75 H HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 H C HIC 75 H HIC 73 1_555 H N GLY 76 H GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 M O1B ADP . A ADP 401 1_555 O MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc2 N O2 PO4 . A PO4 402 1_555 O MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc3 P O2 PO4 . B PO4 401 1_555 R MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc4 Q O1B ADP . B ADP 402 1_555 R MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc5 S O1B ADP . C ADP 401 1_555 T MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? metalc ? metalc6 T MG MG . C MG 402 1_555 U O2 PO4 . C PO4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc7 V MG MG . D MG 801 1_555 W O1B ADP . D ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? metalc ? metalc8 V MG MG . D MG 801 1_555 X O2 PO4 . D PO4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc9 Y MG MG . E MG 801 1_555 Z O1A ADP . E ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? metalc ? metalc10 Y MG MG . E MG 801 1_555 Z O1B ADP . E ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? metalc ? metalc11 Y MG MG . E MG 801 1_555 AA O2 PO4 . E PO4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc12 BA MG MG . F MG 801 1_555 CA O1B ADP . F ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc13 BA MG MG . F MG 801 1_555 DA O2 PO4 . F PO4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc14 EA O2 PO4 . G PO4 401 1_555 GA MG MG . G MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc15 FA O1B ADP . G ADP 402 1_555 GA MG MG . G MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc16 HA MG MG . H MG 801 1_555 IA O2 PO4 . H PO4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc17 HA MG MG . H MG 801 1_555 JA O1B ADP . H ADP 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 8C4C _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 3 ADP A 1 401 802 ADP ADP . N 4 PO4 A 1 402 803 PO4 PO4 . O 5 MG A 1 403 801 MG MG . P 4 PO4 B 1 401 803 PO4 PO4 . Q 3 ADP B 1 402 802 ADP ADP . R 5 MG B 1 403 801 MG MG . S 3 ADP C 1 401 802 ADP ADP . T 5 MG C 1 402 801 MG MG . U 4 PO4 C 1 403 803 PO4 PO4 . V 5 MG D 1 801 801 MG MG . W 3 ADP D 1 802 802 ADP ADP . X 4 PO4 D 1 803 803 PO4 PO4 . Y 5 MG E 1 801 801 MG MG . Z 3 ADP E 1 802 802 ADP ADP . AA 4 PO4 E 1 803 803 PO4 PO4 . BA 5 MG F 1 801 801 MG MG . CA 3 ADP F 1 802 802 ADP ADP . DA 4 PO4 F 1 803 803 PO4 PO4 . EA 4 PO4 G 1 401 803 PO4 PO4 . FA 3 ADP G 1 402 802 ADP ADP . GA 5 MG G 1 403 801 MG MG . HA 5 MG H 1 801 801 MG MG . IA 4 PO4 H 1 802 803 PO4 PO4 . JA 3 ADP H 1 803 802 ADP ADP . # 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 PB ADP . . . Z 3 228.25 210.398 197.66 1 50.85 ? PB ADP 802 E 1 HETATM 2 O O1B ADP . . . Z 3 228.966 210.269 196.338 1 67.17 ? O1B ADP 802 E 1 HETATM 3 O O2B ADP . . . Z 3 229.144 210.752 198.821 1 47.45 ? O2B ADP 802 E 1 HETATM 4 O O3B ADP . . . Z 3 226.963 211.179 197.606 1 55.72 ? O3B ADP 802 E 1 HETATM 5 P PA ADP . . . Z 3 228.85 207.717 198.112 1 38.47 ? PA ADP 802 E 1 HETATM 6 O O1A ADP . . . Z 3 229.12 207.159 196.738 1 53.68 ? O1A ADP 802 E 1 HETATM 7 O O2A ADP . . . Z 3 229.97 208.199 198.997 1 54.15 ? O2A ADP 802 E 1 HETATM 8 O O3A ADP . . . Z 3 227.776 208.902 197.983 1 51.56 ? O3A ADP 802 E 1 HETATM 9 O O5' ADP . . . Z 3 227.963 206.671 198.937 1 54.55 ? O5' ADP 802 E 1 HETATM 10 C C5' ADP . . . Z 3 227.586 206.978 200.273 1 51.53 ? C5' ADP 802 E 1 HETATM 11 C C4' ADP . . . Z 3 226.246 206.312 200.529 1 45.41 ? C4' ADP 802 E 1 HETATM 12 O O4' ADP . . . Z 3 226.326 204.953 200.104 1 58.58 ? O4' ADP 802 E 1 HETATM 13 C C3' ADP . . . Z 3 225.858 206.332 201.996 1 48.41 ? C3' ADP 802 E 1 HETATM 14 O O3' ADP . . . Z 3 224.632 207.046 202.17 1 54.07 ? O3' ADP 802 E 1 HETATM 15 C C2' ADP . . . Z 3 225.7 204.88 202.396 1 57.06 ? C2' ADP 802 E 1 HETATM 16 O O2' ADP . . . Z 3 224.413 204.655 202.97 1 67.34 ? O2' ADP 802 E 1 HETATM 17 C C1' ADP . . . Z 3 225.867 204.069 201.121 1 52.02 ? C1' ADP 802 E 1 HETATM 18 N N9 ADP . . . Z 3 226.868 202.993 201.307 1 50.04 ? N9 ADP 802 E 1 HETATM 19 C C8 ADP . . . Z 3 228.189 203.184 201.468 1 49.39 ? C8 ADP 802 E 1 HETATM 20 N N7 ADP . . . Z 3 228.832 201.998 201.609 1 46.54 ? N7 ADP 802 E 1 HETATM 21 C C5 ADP . . . Z 3 227.91 201.026 201.539 1 45.23 ? C5 ADP 802 E 1 HETATM 22 C C6 ADP . . . Z 3 227.911 199.55 201.611 1 49.67 ? C6 ADP 802 E 1 HETATM 23 N N6 ADP . . . Z 3 229.06 198.858 201.795 1 58.46 ? N6 ADP 802 E 1 HETATM 24 N N1 ADP . . . Z 3 226.727 198.916 201.49 1 49.14 ? N1 ADP 802 E 1 HETATM 25 C C2 ADP . . . Z 3 225.574 199.583 201.307 1 50.48 ? C2 ADP 802 E 1 HETATM 26 N N3 ADP . . . Z 3 225.504 200.923 201.231 1 43.53 ? N3 ADP 802 E 1 HETATM 27 C C4 ADP . . . Z 3 226.615 201.686 201.338 1 49.12 ? C4 ADP 802 E 1 HETATM 28 H "H5'1" ADP . . . Z 3 227.501 208.059 200.402 1 52.7 ? "H5'1" ADP 802 E 1 HETATM 29 H "H5'2" ADP . . . Z 3 228.334 206.601 200.975 1 52.48 ? "H5'2" ADP 802 E 1 HETATM 30 H H4' ADP . . . Z 3 225.475 206.84 199.95 1 51.77 ? H4' ADP 802 E 1 HETATM 31 H H3' ADP . . . Z 3 226.663 206.793 202.585 1 52.53 ? H3' ADP 802 E 1 HETATM 32 H HO3' ADP . . . Z 3 224.471 207.191 203.113 1 53.91 ? HO3' ADP 802 E 1 HETATM 33 H H2' ADP . . . Z 3 226.492 204.614 203.109 1 52.98 ? H2' ADP 802 E 1 HETATM 34 H HO2' ADP . . . Z 3 224.352 205.123 203.812 1 54.32 ? HO2' ADP 802 E 1 HETATM 35 H H1' ADP . . . Z 3 224.896 203.64 200.838 1 52.46 ? H1' ADP 802 E 1 HETATM 36 H H8 ADP . . . Z 3 228.673 204.153 201.482 1 52.62 ? H8 ADP 802 E 1 HETATM 37 H HN61 ADP . . . Z 3 229.038 197.85 201.842 1 53.05 ? HN61 ADP 802 E 1 HETATM 38 H HN62 ADP . . . Z 3 229.937 199.35 201.884 1 53.36 ? HN62 ADP 802 E 1 HETATM 39 H H2 ADP . . . Z 3 224.661 199.012 201.217 1 52.08 ? H2 ADP 802 E 1 # _model_server_stats.io_time_ms 227 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 55 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #