data_9E8J # _model_server_result.job_id JNhB6zIToWgQuFpZFyyGgA _model_server_result.datetime_utc '2024-12-20 19:47:44' _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 9e8j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"IA","auth_seq_id":501}' # _entry.id 9E8J # _exptl.entry_id 9E8J _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 31 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 28-meric _pdbx_struct_assembly.oligomeric_count 28 _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,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA _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 ? 31 IA N N ? 31 KA 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 G SG CYS 115 G CYS 115 1_555 G SG CYS 154 G CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 H SG CYS 137 H CYS 137 1_555 H SG CYS 213 H CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 M SG CYS 42 M CYS 41 1_555 M SG CYS 187 M CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 N SG CYS 633 U CYS 633 1_555 N SG CYS 659 U CYS 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A OG1 THR 223 A THR 223 1_555 DA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.729 ? metalc ? metalc2 A OD2 ASP 275 A ASP 275 1_555 DA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? metalc ? metalc3 CA O1B ATP . A ATP 501 1_555 DA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc4 B OG1 THR 233 B THR 233 1_555 FA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc5 B OD2 ASP 285 B ASP 285 1_555 FA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc6 EA O2G ATP . B ATP 501 1_555 FA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc7 EA O2B ATP . B ATP 501 1_555 FA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc8 C OD1 ASP 249 C ASP 249 1_555 HA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc9 C OD2 ASP 249 C ASP 249 1_555 HA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc10 GA O1G ATP . C ATP 501 1_555 HA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc11 GA O2G ATP . C ATP 501 1_555 HA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc12 D OG1 THR 213 D THR 213 1_555 JA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.77 ? metalc ? metalc13 D OD2 ASP 265 D ASP 265 1_555 JA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? metalc ? metalc14 IA O2B ADP . D ADP 501 1_555 JA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.832 ? metalc ? metalc15 IA O3A ADP . D ADP 501 1_555 JA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc16 F OG1 THR 234 F THR 234 1_555 MA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc17 LA O3G ATP . F ATP 501 1_555 MA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc18 V NE2 HIS 113 c HIS 113 1_555 NA ZN ZN . u ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc19 V NE2 HIS 115 c HIS 115 1_555 NA ZN ZN . u ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc20 V OD1 ASP 126 c ASP 126 1_555 NA ZN ZN . u ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc21 V OD2 ASP 126 c ASP 126 1_555 NA ZN ZN . u ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.778 ? metalc ? metalc22 AA ND1 HIS 289 u HIS 289 1_555 NA ZN ZN . u ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc23 AA NE2 HIS 289 u HIS 289 1_555 NA ZN ZN . u ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? # _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 9E8J _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 CA 29 ATP A 1 501 501 ATP ATP . DA 30 MG A 1 502 502 MG MG . EA 29 ATP B 1 501 501 ATP ATP . FA 30 MG B 1 502 502 MG MG . GA 29 ATP C 1 501 501 ATP ATP . HA 30 MG C 1 502 502 MG MG . IA 31 ADP D 1 501 501 ADP ADP . JA 30 MG D 1 502 502 MG MG . KA 31 ADP E 1 501 501 ADP ADP . LA 29 ATP F 1 501 501 ATP ATP . MA 30 MG F 1 502 502 MG MG . NA 32 ZN u 1 301 311 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 PB ADP . . . IA 31 166.415 175.276 170.685 1 39.63 ? PB ADP 501 D 1 HETATM 2 O O1B ADP . . . IA 31 166.702 173.807 170.557 1 39.63 ? O1B ADP 501 D 1 HETATM 3 O O2B ADP . . . IA 31 167.656 176.111 170.834 1 39.63 ? O2B ADP 501 D 1 HETATM 4 O O3B ADP . . . IA 31 165.39 175.573 171.742 1 39.63 ? O3B ADP 501 D 1 HETATM 5 P PA ADP . . . IA 31 164.689 174.982 168.353 1 39.63 ? PA ADP 501 D 1 HETATM 6 O O1A ADP . . . IA 31 163.463 174.632 169.12 1 39.63 ? O1A ADP 501 D 1 HETATM 7 O O2A ADP . . . IA 31 165.398 173.875 167.65 1 39.63 ? O2A ADP 501 D 1 HETATM 8 O O3A ADP . . . IA 31 165.736 175.725 169.302 1 39.63 ? O3A ADP 501 D 1 HETATM 9 O O5' ADP . . . IA 31 164.351 176.14 167.3 1 39.63 ? O5' ADP 501 D 1 HETATM 10 C C5' ADP . . . IA 31 163.097 176.021 166.589 1 39.63 ? C5' ADP 501 D 1 HETATM 11 C C4' ADP . . . IA 31 163.301 176.24 165.11 1 39.63 ? C4' ADP 501 D 1 HETATM 12 O O4' ADP . . . IA 31 162.603 175.202 164.375 1 39.63 ? O4' ADP 501 D 1 HETATM 13 C C3' ADP . . . IA 31 162.765 177.569 164.568 1 39.63 ? C3' ADP 501 D 1 HETATM 14 O O3' ADP . . . IA 31 163.837 178.445 164.247 1 39.63 ? O3' ADP 501 D 1 HETATM 15 C C2' ADP . . . IA 31 161.972 177.179 163.317 1 39.63 ? C2' ADP 501 D 1 HETATM 16 O O2' ADP . . . IA 31 162.743 177.211 162.139 1 39.63 ? O2' ADP 501 D 1 HETATM 17 C C1' ADP . . . IA 31 161.542 175.753 163.631 1 39.63 ? C1' ADP 501 D 1 HETATM 18 N N9 ADP . . . IA 31 160.324 175.637 164.422 1 39.63 ? N9 ADP 501 D 1 HETATM 19 C C8 ADP . . . IA 31 160.112 174.716 165.413 1 39.63 ? C8 ADP 501 D 1 HETATM 20 N N7 ADP . . . IA 31 158.938 174.815 165.978 1 39.63 ? N7 ADP 501 D 1 HETATM 21 C C5 ADP . . . IA 31 158.332 175.871 165.32 1 39.63 ? C5 ADP 501 D 1 HETATM 22 C C6 ADP . . . IA 31 157.069 176.466 165.47 1 39.63 ? C6 ADP 501 D 1 HETATM 23 N N6 ADP . . . IA 31 156.165 176.065 166.357 1 39.63 ? N6 ADP 501 D 1 HETATM 24 N N1 ADP . . . IA 31 156.768 177.503 164.656 1 39.63 ? N1 ADP 501 D 1 HETATM 25 C C2 ADP . . . IA 31 157.682 177.897 163.765 1 39.63 ? C2 ADP 501 D 1 HETATM 26 N N3 ADP . . . IA 31 158.897 177.412 163.535 1 39.63 ? N3 ADP 501 D 1 HETATM 27 C C4 ADP . . . IA 31 159.174 176.389 164.358 1 39.63 ? C4 ADP 501 D 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 390 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #