data_8DVU # _model_server_result.job_id Ap4U20dh6wiWhGBZCuJVTA _model_server_result.datetime_utc '2024-10-19 11:24:28' _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 8dvu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1003}' # _entry.id 8DVU # _exptl.entry_id 8DVU _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 8DVU _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DVU _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 5 _struct_asym.id E _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 A SG CYS 810 A CYS 810 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc2 A SG CYS 813 A CYS 813 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc3 A SG CYS 864 A CYS 864 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc4 A SG CYS 869 A CYS 869 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc5 D MG MG . A MG 1002 1_555 E O2B ADP . A ADP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? hydrog WATSON-CRICK hydrog1 B N1 G 6 B G 6 1_555 B N3 C 59 B C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 G 6 B G 6 1_555 B O2 C 59 B C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 G 6 B G 6 1_555 B N4 C 59 B C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 A 7 B A 7 1_555 B N3 U 58 B U 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 A 7 B A 7 1_555 B O4 U 58 B U 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 U 8 B U 8 1_555 B N1 A 57 B A 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 U 8 B U 8 1_555 B N6 A 57 B A 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 C 9 B C 9 1_555 B N1 G 56 B G 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 C 9 B C 9 1_555 B O6 G 56 B G 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 C 9 B C 9 1_555 B N2 G 56 B G 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 G 10 B G 10 1_555 B N3 C 55 B C 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N2 G 10 B G 10 1_555 B O2 C 55 B C 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O6 G 10 B G 10 1_555 B N4 C 55 B C 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 A 11 B A 11 1_555 B N3 U 54 B U 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 A 11 B A 11 1_555 B O4 U 54 B U 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 U 12 B U 12 1_555 B N1 A 53 B A 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O4 U 12 B U 12 1_555 B N6 A 53 B A 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 C 13 B C 13 1_555 B N1 G 52 B G 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N4 C 13 B C 13 1_555 B O6 G 52 B G 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O2 C 13 B C 13 1_555 B N2 G 52 B G 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N1 G 14 B G 14 1_555 B N3 C 51 B C 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N2 G 14 B G 14 1_555 B O2 C 51 B C 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O6 G 14 B G 14 1_555 B N4 C 51 B C 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N1 A 15 B A 15 1_555 B N3 U 50 B U 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N6 A 15 B A 15 1_555 B O4 U 50 B U 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N3 U 16 B U 16 1_555 B N1 A 49 B A 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B O4 U 16 B U 16 1_555 B N6 A 49 B A 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N3 C 17 B C 17 1_555 B N1 G 48 B G 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N4 C 17 B C 17 1_555 B O6 G 48 B G 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B O2 C 17 B C 17 1_555 B N2 G 48 B G 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N1 G 18 B G 18 1_555 B N3 C 47 B C 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B N2 G 18 B G 18 1_555 B O2 C 47 B C 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B O6 G 18 B G 18 1_555 B N4 C 47 B C 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B N1 G 19 B G 19 1_555 B N3 C 46 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N2 G 19 B G 19 1_555 B O2 C 46 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B O6 G 19 B G 19 1_555 B N4 C 46 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 B N3 C 20 B C 20 1_555 B N1 G 45 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 B N4 C 20 B C 20 1_555 B O6 G 45 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 B O2 C 20 B C 20 1_555 B N2 G 45 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 B N1 A 21 B A 21 1_555 B N3 U 44 B U 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 B N6 A 21 B A 21 1_555 B O4 U 44 B U 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 B N3 U 22 B U 22 1_555 B N1 A 43 B A 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 B O4 U 22 B U 22 1_555 B N6 A 43 B A 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 B N3 C 23 B C 23 1_555 B N1 G 42 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 B N4 C 23 B C 23 1_555 B O6 G 42 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 B O2 C 23 B C 23 1_555 B N2 G 42 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 40 n n PB O2B ADP sing 41 n n PB O3B ADP sing 42 n n PB O3A ADP sing 43 n n O2B HOB2 ADP sing 44 n n O3B HOB3 ADP sing 45 n n PA O1A ADP doub 46 n n PA O2A ADP sing 47 n n PA O3A ADP sing 48 n n PA O5' ADP sing 49 n n O2A HOA2 ADP sing 50 n n O5' C5' ADP sing 51 n n C5' C4' ADP sing 52 n n C5' "H5'1" ADP sing 53 n n C5' "H5'2" ADP sing 54 n n C4' O4' ADP sing 55 n n C4' C3' ADP sing 56 n n C4' H4' ADP sing 57 n n O4' C1' ADP sing 58 n n C3' O3' ADP sing 59 n n C3' C2' ADP sing 60 n n C3' H3' ADP sing 61 n n O3' HO3' ADP sing 62 n n C2' O2' ADP sing 63 n n C2' C1' ADP sing 64 n n C2' H2' ADP sing 65 n n O2' HO2' ADP sing 66 n n C1' N9 ADP sing 67 n n C1' H1' ADP sing 68 n n N9 C8 ADP sing 69 n y N9 C4 ADP sing 70 n y C8 N7 ADP doub 71 n y C8 H8 ADP sing 72 n n N7 C5 ADP sing 73 n y C5 C6 ADP sing 74 n y C5 C4 ADP doub 75 n y C6 N6 ADP sing 76 n n C6 N1 ADP doub 77 n y N6 HN61 ADP sing 78 n n N6 HN62 ADP sing 79 n n N1 C2 ADP sing 80 n y C2 N3 ADP doub 81 n y C2 H2 ADP sing 82 n n N3 C4 ADP sing 83 n y # _atom_sites.entry_id 8DVU _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 C 3 ZN A 1 1001 1001 ZN ZN . D 4 MG A 1 1002 1003 MG MG . E 5 ADP A 1 1003 1006 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 . . . E 5 109.604 122.744 91.461 1 20.91 ? PB ADP 1003 A 1 HETATM 2 O O1B ADP . . . E 5 110.246 124.1 91.321 1 20.91 ? O1B ADP 1003 A 1 HETATM 3 O O2B ADP . . . E 5 110.538 121.652 91.919 1 20.91 ? O2B ADP 1003 A 1 HETATM 4 O O3B ADP . . . E 5 108.279 122.767 92.178 1 20.91 ? O3B ADP 1003 A 1 HETATM 5 P PA ADP . . . E 5 110.304 122.258 88.775 1 20.91 ? PA ADP 1003 A 1 HETATM 6 O O1A ADP . . . E 5 110.301 120.857 88.214 1 20.91 ? O1A ADP 1003 A 1 HETATM 7 O O2A ADP . . . E 5 111.603 122.843 89.27 1 20.91 ? O2A ADP 1003 A 1 HETATM 8 O O3A ADP . . . E 5 109.215 122.307 89.961 1 20.91 ? O3A ADP 1003 A 1 HETATM 9 O O5' ADP . . . E 5 109.696 123.23 87.647 1 20.91 ? O5' ADP 1003 A 1 HETATM 10 C C5' ADP . . . E 5 109.58 124.633 87.857 1 20.91 ? C5' ADP 1003 A 1 HETATM 11 C C4' ADP . . . E 5 109.326 125.301 86.512 1 20.91 ? C4' ADP 1003 A 1 HETATM 12 O O4' ADP . . . E 5 109.513 126.712 86.625 1 20.91 ? O4' ADP 1003 A 1 HETATM 13 C C3' ADP . . . E 5 110.301 124.8 85.459 1 20.91 ? C3' ADP 1003 A 1 HETATM 14 O O3' ADP . . . E 5 109.603 124.053 84.459 1 20.91 ? O3' ADP 1003 A 1 HETATM 15 C C2' ADP . . . E 5 110.924 126.033 84.839 1 20.91 ? C2' ADP 1003 A 1 HETATM 16 O O2' ADP . . . E 5 110.677 126.047 83.431 1 20.91 ? O2' ADP 1003 A 1 HETATM 17 C C1' ADP . . . E 5 110.243 127.216 85.505 1 20.91 ? C1' ADP 1003 A 1 HETATM 18 N N9 ADP . . . E 5 111.26 128.195 85.961 1 20.91 ? N9 ADP 1003 A 1 HETATM 19 C C8 ADP . . . E 5 112.064 128.054 87.031 1 20.91 ? C8 ADP 1003 A 1 HETATM 20 N N7 ADP . . . E 5 112.88 129.127 87.174 1 20.91 ? N7 ADP 1003 A 1 HETATM 21 C C5 ADP . . . E 5 112.602 129.983 86.175 1 20.91 ? C5 ADP 1003 A 1 HETATM 22 C C6 ADP . . . E 5 113.095 131.309 85.735 1 20.91 ? C6 ADP 1003 A 1 HETATM 23 N N6 ADP . . . E 5 114.077 131.952 86.41 1 20.91 ? N6 ADP 1003 A 1 HETATM 24 N N1 ADP . . . E 5 112.532 131.855 84.636 1 20.91 ? N1 ADP 1003 A 1 HETATM 25 C C2 ADP . . . E 5 111.556 131.228 83.954 1 20.91 ? C2 ADP 1003 A 1 HETATM 26 N N3 ADP . . . E 5 111.061 130.026 84.296 1 20.91 ? N3 ADP 1003 A 1 HETATM 27 C C4 ADP . . . E 5 111.534 129.363 85.377 1 20.91 ? C4 ADP 1003 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #