data_9E8Q # _model_server_result.job_id m-8Qzse01hdQkj6tXh9WwA _model_server_result.datetime_utc '2024-12-28 01:45:53' _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 9e8q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"MA","auth_seq_id":501}' # _entry.id 9E8Q # _exptl.entry_id 9E8Q _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 34 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 33-meric _pdbx_struct_assembly.oligomeric_count 33 _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,OA,PA,QA _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 ? 34 HA N N ? 34 MA N N ? 34 OA N N ? 34 PA 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 F SG CYS 396 F CYS 396 1_555 F SG CYS 400 F CYS 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf2 U SG CYS 633 U CYS 633 1_555 U SG CYS 659 U CYS 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 B OG1 THR 233 B THR 233 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc2 IA O1G ATP . B ATP 501 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc3 IA O2G ATP . B ATP 501 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc4 IA O1B ATP . B ATP 501 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? metalc ? metalc5 IA O3B ATP . B ATP 501 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc6 IA O3A ATP . B ATP 501 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc7 C OG1 THR 197 C THR 197 1_555 LA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.872 ? metalc ? metalc8 KA O2G ATP . C ATP 501 1_555 LA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc9 D OG1 THR 213 D THR 213 1_555 NA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc10 MA O2B ADP . D ADP 501 1_555 NA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? metalc ? metalc11 MA O3B ADP . D ADP 501 1_555 NA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc12 CA NE2 HIS 113 c HIS 113 1_555 QA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc13 CA NE2 HIS 115 c HIS 115 1_555 QA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc14 CA OD1 ASP 126 c ASP 126 1_555 QA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc15 CA OD2 ASP 126 c ASP 126 1_555 QA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? # _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 9E8Q _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 HA 34 ADP A 1 501 501 ADP ADP . IA 35 ATP B 1 501 501 ATP ATP . JA 36 MG B 1 502 502 MG MG . KA 35 ATP C 1 501 501 ATP ATP . LA 36 MG C 1 502 502 MG MG . MA 34 ADP D 1 501 501 ADP ADP . NA 36 MG D 1 502 502 MG MG . OA 34 ADP E 1 501 501 ADP ADP . PA 34 ADP F 1 501 501 ADP ADP . QA 37 ZN c 1 501 401 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 . . . MA 34 160.862 160.071 169.188 1 35.29 ? PB ADP 501 D 1 HETATM 2 O O1B ADP . . . MA 34 159.812 159.168 169.776 1 28.99 ? O1B ADP 501 D 1 HETATM 3 O O2B ADP . . . MA 34 161.027 161.377 169.908 1 38.75 ? O2B ADP 501 D 1 HETATM 4 O O3B ADP . . . MA 34 162.157 159.381 168.85 1 34.32 ? O3B ADP 501 D 1 HETATM 5 P PA ADP . . . MA 34 158.823 161.208 167.678 1 29.15 ? PA ADP 501 D 1 HETATM 6 O O1A ADP . . . MA 34 157.825 160.312 168.356 1 31.25 ? O1A ADP 501 D 1 HETATM 7 O O2A ADP . . . MA 34 158.95 162.638 168.105 1 22.48 ? O2A ADP 501 D 1 HETATM 8 O O3A ADP . . . MA 34 160.258 160.5 167.765 1 30.27 ? O3A ADP 501 D 1 HETATM 9 O O5' ADP . . . MA 34 158.473 161.219 166.118 1 28.67 ? O5' ADP 501 D 1 HETATM 10 C C5' ADP . . . MA 34 157.174 161.661 165.761 1 24.6 ? C5' ADP 501 D 1 HETATM 11 C C4' ADP . . . MA 34 156.909 161.477 164.279 1 28.57 ? C4' ADP 501 D 1 HETATM 12 O O4' ADP . . . MA 34 155.875 160.512 164.117 1 29.95 ? O4' ADP 501 D 1 HETATM 13 C C3' ADP . . . MA 34 156.418 162.775 163.679 1 29.96 ? C3' ADP 501 D 1 HETATM 14 O O3' ADP . . . MA 34 157.182 163.089 162.518 1 35.72 ? O3' ADP 501 D 1 HETATM 15 C C2' ADP . . . MA 34 154.984 162.537 163.281 1 31.87 ? C2' ADP 501 D 1 HETATM 16 O O2' ADP . . . MA 34 154.848 162.759 161.879 1 45.9 ? O2' ADP 501 D 1 HETATM 17 C C1' ADP . . . MA 34 154.675 161.096 163.623 1 28.45 ? C1' ADP 501 D 1 HETATM 18 N N9 ADP . . . MA 34 153.715 161.029 164.745 1 29.8 ? N9 ADP 501 D 1 HETATM 19 C C8 ADP . . . MA 34 153.965 160.384 165.892 1 35.02 ? C8 ADP 501 D 1 HETATM 20 N N7 ADP . . . MA 34 152.922 160.47 166.748 1 34.67 ? N7 ADP 501 D 1 HETATM 21 C C5 ADP . . . MA 34 151.969 161.185 166.141 1 28.46 ? C5 ADP 501 D 1 HETATM 22 C C6 ADP . . . MA 34 150.616 161.637 166.499 1 30.24 ? C6 ADP 501 D 1 HETATM 23 N N6 ADP . . . MA 34 150.076 161.334 167.699 1 31.51 ? N6 ADP 501 D 1 HETATM 24 N N1 ADP . . . MA 34 149.943 162.363 165.589 1 35.13 ? N1 ADP 501 D 1 HETATM 25 C C2 ADP . . . MA 34 150.48 162.664 164.396 1 36.99 ? C2 ADP 501 D 1 HETATM 26 N N3 ADP . . . MA 34 151.706 162.285 164.004 1 35.43 ? N3 ADP 501 D 1 HETATM 27 C C4 ADP . . . MA 34 152.486 161.541 164.815 1 29.76 ? C4 ADP 501 D 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 497 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #