data_8USB # _model_server_result.job_id YSqOAeOuSDt2Sg_TnM5mJg _model_server_result.datetime_utc '2024-11-07 03:37:58' _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 8usb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"BA","auth_seq_id":501}' # _entry.id 8USB # _exptl.entry_id 8USB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 28 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 8USB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8USB _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 27-meric _pdbx_struct_assembly.oligomeric_count 27 _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,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 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 # _struct_asym.details ? _struct_asym.entity_id 28 _struct_asym.id BA _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 L SG CYS 115 G CYS 115 1_555 L SG CYS 154 G CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc1 BA O2B ADP . C ADP 501 1_555 CA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc2 BA O3B ADP . C ADP 501 1_555 CA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc3 G OG1 THR 233 B THR 233 1_555 EA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc4 DA O1G ATP . B ATP 501 1_555 EA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc5 H OG1 THR 223 A THR 223 1_555 GA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc6 FA O3G ATP . A ATP 501 1_555 GA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc7 FA O2B ATP . A ATP 501 1_555 GA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc8 I OG1 THR 213 D THR 213 1_555 IA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc9 HA O3G ATP . D ATP 501 1_555 IA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc10 HA O2B ATP . D ATP 501 1_555 IA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc11 J OG1 THR 181 E THR 181 1_555 KA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc12 JA O2G ATP . E ATP 501 1_555 KA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc13 JA O2B ATP . E ATP 501 1_555 KA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc14 K OG1 THR 234 F THR 234 1_555 MA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc15 LA O3G ATP . F ATP 501 1_555 MA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc16 LA O2B ATP . F ATP 501 1_555 MA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc17 V OE1 GLU 52 c GLU 52 1_555 NA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc18 V NE2 HIS 113 c HIS 113 1_555 NA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc19 V NE2 HIS 115 c HIS 115 1_555 NA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc20 V OD2 ASP 126 c ASP 126 1_555 NA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? # _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 8USB _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 BA 28 ADP C 1 501 501 ADP ADP . CA 29 MG C 1 502 502 MG MG . DA 30 ATP B 1 501 501 ATP ATP . EA 29 MG B 1 502 502 MG MG . FA 30 ATP A 1 501 501 ATP ATP . GA 29 MG A 1 502 502 MG MG . HA 30 ATP D 1 501 501 ATP ATP . IA 29 MG D 1 502 502 MG MG . JA 30 ATP E 1 501 501 ATP ATP . KA 29 MG E 1 502 502 MG MG . LA 30 ATP F 1 501 501 ATP ATP . MA 29 MG F 1 502 502 MG MG . NA 31 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 . . . BA 28 130.595 142.744 162.917 1 108 ? PB ADP 501 C 1 HETATM 2 O O1B ADP . . . BA 28 130.008 142.565 164.293 1 95.26 ? O1B ADP 501 C 1 HETATM 3 O O2B ADP . . . BA 28 130.78 141.463 162.144 1 102.51 ? O2B ADP 501 C 1 HETATM 4 O O3B ADP . . . BA 28 131.772 143.685 162.855 1 102.54 ? O3B ADP 501 C 1 HETATM 5 P PA ADP . . . BA 28 129.307 145.119 162.163 1 98.69 ? PA ADP 501 C 1 HETATM 6 O O1A ADP . . . BA 28 129.17 145.557 163.599 1 91.79 ? O1A ADP 501 C 1 HETATM 7 O O2A ADP . . . BA 28 130.4 145.688 161.294 1 103.79 ? O2A ADP 501 C 1 HETATM 8 O O3A ADP . . . BA 28 129.437 143.518 162.117 1 99.48 ? O3A ADP 501 C 1 HETATM 9 O O5' ADP . . . BA 28 127.897 145.348 161.429 1 90.57 ? O5' ADP 501 C 1 HETATM 10 C C5' ADP . . . BA 28 127.798 146.23 160.316 1 95.27 ? C5' ADP 501 C 1 HETATM 11 C C4' ADP . . . BA 28 126.471 146.968 160.387 1 94.3 ? C4' ADP 501 C 1 HETATM 12 O O4' ADP . . . BA 28 125.437 146.086 160.824 1 90.77 ? O4' ADP 501 C 1 HETATM 13 C C3' ADP . . . BA 28 126.544 148.1 161.394 1 90.62 ? C3' ADP 501 C 1 HETATM 14 O O3' ADP . . . BA 28 126.547 149.36 160.719 1 109.26 ? O3' ADP 501 C 1 HETATM 15 C C2' ADP . . . BA 28 125.301 147.977 162.246 1 88.35 ? C2' ADP 501 C 1 HETATM 16 O O2' ADP . . . BA 28 124.485 149.136 162.065 1 95.56 ? O2' ADP 501 C 1 HETATM 17 C C1' ADP . . . BA 28 124.572 146.742 161.751 1 85.36 ? C1' ADP 501 C 1 HETATM 18 N N9 ADP . . . BA 28 124.314 145.848 162.903 1 81.57 ? N9 ADP 501 C 1 HETATM 19 C C8 ADP . . . BA 28 124.912 144.666 163.127 1 85.7 ? C8 ADP 501 C 1 HETATM 20 N N7 ADP . . . BA 28 124.456 144.094 164.269 1 83.73 ? N7 ADP 501 C 1 HETATM 21 C C5 ADP . . . BA 28 123.542 144.926 164.796 1 74.85 ? C5 ADP 501 C 1 HETATM 22 C C6 ADP . . . BA 28 122.674 144.933 165.993 1 77.79 ? C6 ADP 501 C 1 HETATM 23 N N6 ADP . . . BA 28 122.694 143.909 166.878 1 80.1 ? N6 ADP 501 C 1 HETATM 24 N N1 ADP . . . BA 28 121.862 145.994 166.174 1 81.78 ? N1 ADP 501 C 1 HETATM 25 C C2 ADP . . . BA 28 121.832 147.016 165.302 1 79.26 ? C2 ADP 501 C 1 HETATM 26 N N3 ADP . . . BA 28 122.592 147.076 164.197 1 75.24 ? N3 ADP 501 C 1 HETATM 27 C C4 ADP . . . BA 28 123.451 146.078 163.892 1 74.55 ? C4 ADP 501 C 1 # _model_server_stats.io_time_ms 102 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 468 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #