data_7Y5C # _model_server_result.job_id XB1sW1UyWVTIYo-poVpPbw _model_server_result.datetime_utc '2024-10-11 04:23:00' _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 7y5c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"CA","auth_seq_id":501}' # _entry.id 7Y5C # _exptl.entry_id 7Y5C _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 11 _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 7Y5C _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Y5C _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 eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 11 _struct_asym.id CA _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 metalc ? metalc1 U MG MG . A MG 600 1_555 V O1A ATP . A ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc2 U MG MG . A MG 600 1_555 V O2A ATP . A ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc3 U MG MG . A MG 600 1_555 V O3A ATP . A ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc4 U MG MG . A MG 600 1_555 V O1B ATP . A ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc5 U MG MG . A MG 600 1_555 V O1G ATP . A ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc6 U MG MG . A MG 600 1_555 V O3G ATP . A ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc7 U MG MG . A MG 600 1_555 V O3B ATP . A ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc8 W MG MG . B MG 600 1_555 X O1B ATP . B ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc9 W MG MG . B MG 600 1_555 X O3B ATP . B ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc10 W MG MG . B MG 600 1_555 X O2A ATP . B ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc11 W MG MG . B MG 600 1_555 X O3G ATP . B ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc12 W MG MG . B MG 600 1_555 X O1A ATP . B ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc13 W MG MG . B MG 600 1_555 X O3A ATP . B ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc14 W MG MG . B MG 600 1_555 X O1G ATP . B ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc15 C OG1 THR 179 C THR 179 1_555 Y MG MG . C MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc16 Y MG MG . C MG 600 1_555 Z O1A ATP . C ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc17 Y MG MG . C MG 600 1_555 Z O3A ATP . C ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc18 Y MG MG . C MG 600 1_555 Z O1B ATP . C ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc19 Y MG MG . C MG 600 1_555 Z O3B ATP . C ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc20 Y MG MG . C MG 600 1_555 Z O3G ATP . C ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc21 Y MG MG . C MG 600 1_555 Z O1G ATP . C ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.919 ? metalc ? metalc22 D OG1 THR 173 D THR 167 1_555 AA MG MG . D MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc23 AA MG MG . D MG 500 1_555 BA O2A ATP . D ATP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc24 AA MG MG . D MG 500 1_555 BA O3A ATP . D ATP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc25 AA MG MG . D MG 500 1_555 BA O1B ATP . D ATP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc26 AA MG MG . D MG 500 1_555 BA O1A ATP . D ATP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc27 F OG1 THR 173 F THR 167 1_555 DA MG MG . F MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc28 DA MG MG . F MG 500 1_555 EA O1B ATP . F ATP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc29 DA MG MG . F MG 500 1_555 EA O2G ATP . F ATP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc30 DA MG MG . F MG 500 1_555 EA O3B ATP . F ATP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? # _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 7Y5C _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 U 9 MG A 1 600 600 MG MG . V 10 ATP A 1 601 601 ATP ATP . W 9 MG B 1 600 600 MG MG . X 10 ATP B 1 601 601 ATP ATP . Y 9 MG C 1 600 600 MG MG . Z 10 ATP C 1 601 601 ATP ATP . AA 9 MG D 1 500 500 MG MG . BA 10 ATP D 1 501 501 ATP ATP . CA 11 ADP E 1 501 501 ADP ADP . DA 9 MG F 1 500 500 MG MG . EA 10 ATP F 1 501 501 ATP ATP . # 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 . . . CA 11 231.656 219.092 287.403 1 170.66 ? PB ADP 501 E 1 HETATM 2 O O1B ADP . . . CA 11 230.853 219.91 286.421 1 170.66 ? O1B ADP 501 E 1 HETATM 3 O O2B ADP . . . CA 11 231.39 219.425 288.852 1 170.66 ? O2B ADP 501 E 1 HETATM 4 O O3B ADP . . . CA 11 233.121 218.962 287.06 1 170.66 ? O3B ADP 501 E 1 HETATM 5 P PA ADP . . . CA 11 231.14 216.819 285.832 1 170.66 ? PA ADP 501 E 1 HETATM 6 O O1A ADP . . . CA 11 231.877 217.683 284.837 1 170.66 ? O1A ADP 501 E 1 HETATM 7 O O2A ADP . . . CA 11 231.646 215.424 286.11 1 170.66 ? O2A ADP 501 E 1 HETATM 8 O O3A ADP . . . CA 11 231.09 217.591 287.245 1 170.66 ? O3A ADP 501 E 1 HETATM 9 O O5' ADP . . . CA 11 229.597 216.696 285.382 1 170.66 ? O5' ADP 501 E 1 HETATM 10 C C5' ADP . . . CA 11 228.75 217.836 285.26 1 170.66 ? C5' ADP 501 E 1 HETATM 11 C C4' ADP . . . CA 11 227.407 217.408 284.679 1 170.66 ? C4' ADP 501 E 1 HETATM 12 O O4' ADP . . . CA 11 227.524 217.159 283.276 1 170.66 ? O4' ADP 501 E 1 HETATM 13 C C3' ADP . . . CA 11 226.893 216.126 285.316 1 170.66 ? C3' ADP 501 E 1 HETATM 14 O O3' ADP . . . CA 11 225.767 216.405 286.152 1 170.66 ? O3' ADP 501 E 1 HETATM 15 C C2' ADP . . . CA 11 226.473 215.229 284.167 1 170.66 ? C2' ADP 501 E 1 HETATM 16 O O2' ADP . . . CA 11 225.086 214.902 284.277 1 170.66 ? O2' ADP 501 E 1 HETATM 17 C C1' ADP . . . CA 11 226.724 216.034 282.902 1 170.66 ? C1' ADP 501 E 1 HETATM 18 N N9 ADP . . . CA 11 227.448 215.208 281.906 1 170.66 ? N9 ADP 501 E 1 HETATM 19 C C8 ADP . . . CA 11 228.782 215.048 281.853 1 170.66 ? C8 ADP 501 E 1 HETATM 20 N N7 ADP . . . CA 11 229.14 214.234 280.827 1 170.66 ? N7 ADP 501 E 1 HETATM 21 C C5 ADP . . . CA 11 228.011 213.86 280.199 1 170.66 ? C5 ADP 501 E 1 HETATM 22 C C6 ADP . . . CA 11 227.673 213.008 279.037 1 170.66 ? C6 ADP 501 E 1 HETATM 23 N N6 ADP . . . CA 11 228.641 212.383 278.329 1 170.66 ? N6 ADP 501 E 1 HETATM 24 N N1 ADP . . . CA 11 226.37 212.877 278.708 1 170.66 ? N1 ADP 501 E 1 HETATM 25 C C2 ADP . . . CA 11 225.403 213.497 279.409 1 170.66 ? C2 ADP 501 E 1 HETATM 26 N N3 ADP . . . CA 11 225.637 214.285 280.474 1 170.66 ? N3 ADP 501 E 1 HETATM 27 C C4 ADP . . . CA 11 226.899 214.504 280.913 1 170.66 ? C4 ADP 501 E 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #