data_6UBY # _model_server_result.job_id TZQPMkY6CoXnpkBVdpR-3w _model_server_result.datetime_utc '2024-11-14 17:14:25' _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 6uby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":802}' # _entry.id 6UBY # _exptl.entry_id 6UBY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 _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 ? 4 K N N ? 4 M N N ? 4 O N N ? 4 Q N N ? 4 S N N ? 4 U N N ? 4 W 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 metalc ? metalc1 J MG MG . A MG 801 1_555 K O3B ADP . A ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc2 J MG MG . A MG 801 1_555 K O2B ADP . A ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc3 L MG MG . B MG 801 1_555 M O2B ADP . B ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc4 L MG MG . B MG 801 1_555 M O3B ADP . B ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc5 N MG MG . C MG 801 1_555 O O2B ADP . C ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc6 N MG MG . C MG 801 1_555 O O3B ADP . C ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc7 P MG MG . D MG 801 1_555 Q O2B ADP . D ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc8 P MG MG . D MG 801 1_555 Q O3B ADP . D ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc9 R MG MG . E MG 801 1_555 S O2B ADP . E ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc10 R MG MG . E MG 801 1_555 S O3B ADP . E ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc11 T MG MG . F MG 801 1_555 U O2B ADP . F ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc12 T MG MG . F MG 801 1_555 U O3B ADP . F ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc13 V MG MG . G MG 801 1_555 W O3B ADP . G ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc14 V MG MG . G MG 801 1_555 W O2B ADP . G ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? # _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 6UBY _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 J 3 MG A 1 801 801 MG MG . K 4 ADP A 1 802 802 ADP ADP . L 3 MG B 1 801 801 MG MG . M 4 ADP B 1 802 802 ADP ADP . N 3 MG C 1 801 801 MG MG . O 4 ADP C 1 802 802 ADP ADP . P 3 MG D 1 801 801 MG MG . Q 4 ADP D 1 802 802 ADP ADP . R 3 MG E 1 801 801 MG MG . S 4 ADP E 1 802 802 ADP ADP . T 3 MG F 1 801 801 MG MG . U 4 ADP F 1 802 802 ADP ADP . V 3 MG G 1 801 801 MG MG . W 4 ADP G 1 802 802 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 . . . U 4 129.541 148.312 224.579 1 38.03 ? PB ADP 802 F 1 HETATM 2 O O1B ADP . . . U 4 129.01 149.003 223.346 1 38.03 ? O1B ADP 802 F 1 HETATM 3 O O2B ADP . . . U 4 128.476 147.84 225.54 1 38.03 ? O2B ADP 802 F 1 HETATM 4 O O3B ADP . . . U 4 130.706 149.014 225.232 1 38.03 ? O3B ADP 802 F 1 HETATM 5 P PA ADP . . . U 4 129.276 145.848 223.266 1 38.03 ? PA ADP 802 F 1 HETATM 6 O O1A ADP . . . U 4 128.403 146.551 222.253 1 38.03 ? O1A ADP 802 F 1 HETATM 7 O O2A ADP . . . U 4 128.659 144.949 224.311 1 38.03 ? O2A ADP 802 F 1 HETATM 8 O O3A ADP . . . U 4 130.183 146.951 224.008 1 38.03 ? O3A ADP 802 F 1 HETATM 9 O O5' ADP . . . U 4 130.385 145.01 222.461 1 38.03 ? O5' ADP 802 F 1 HETATM 10 C C5' ADP . . . U 4 130.129 144.553 221.136 1 38.03 ? C5' ADP 802 F 1 HETATM 11 C C4' ADP . . . U 4 131.231 143.587 220.73 1 38.03 ? C4' ADP 802 F 1 HETATM 12 O O4' ADP . . . U 4 130.886 142.265 221.148 1 38.03 ? O4' ADP 802 F 1 HETATM 13 C C3' ADP . . . U 4 131.426 143.541 219.224 1 38.03 ? C3' ADP 802 F 1 HETATM 14 O O3' ADP . . . U 4 132.617 144.244 218.859 1 38.03 ? O3' ADP 802 F 1 HETATM 15 C C2' ADP . . . U 4 131.553 142.074 218.872 1 38.03 ? C2' ADP 802 F 1 HETATM 16 O O2' ADP . . . U 4 132.89 141.789 218.451 1 38.03 ? O2' ADP 802 F 1 HETATM 17 C C1' ADP . . . U 4 131.237 141.309 220.146 1 38.03 ? C1' ADP 802 F 1 HETATM 18 N N9 ADP . . . U 4 130.088 140.401 219.9 1 38.03 ? N9 ADP 802 F 1 HETATM 19 C C8 ADP . . . U 4 128.835 140.791 219.601 1 38.03 ? C8 ADP 802 F 1 HETATM 20 N N7 ADP . . . U 4 128.016 139.721 219.43 1 38.03 ? N7 ADP 802 F 1 HETATM 21 C C5 ADP . . . U 4 128.756 138.613 219.622 1 38.03 ? C5 ADP 802 F 1 HETATM 22 C C6 ADP . . . U 4 128.514 137.152 219.591 1 38.03 ? C6 ADP 802 F 1 HETATM 23 N N6 ADP . . . U 4 127.287 136.649 219.316 1 38.03 ? N6 ADP 802 F 1 HETATM 24 N N1 ADP . . . U 4 129.561 136.34 219.849 1 38.03 ? N1 ADP 802 F 1 HETATM 25 C C2 ADP . . . U 4 130.784 136.826 220.123 1 38.03 ? C2 ADP 802 F 1 HETATM 26 N N3 ADP . . . U 4 131.075 138.138 220.167 1 38.03 ? N3 ADP 802 F 1 HETATM 27 C C4 ADP . . . U 4 130.122 139.067 219.927 1 38.03 ? C4 ADP 802 F 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #