data_8DVS # _model_server_result.job_id zF2yBK9npeD4WC7EEZNyHQ _model_server_result.datetime_utc '2024-10-19 10:30:24' _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 8dvs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1003}' # _entry.id 8DVS # _exptl.entry_id 8DVS _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 8DVS _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DVS _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 OD2 ASP 372 A ASP 372 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc2 A SG CYS 810 A CYS 810 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc3 A SG CYS 864 A CYS 864 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc4 A SG CYS 869 A CYS 869 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? hydrog WATSON-CRICK hydrog1 B N1 G 1 B G 1 1_555 B N3 C 64 B C 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 G 1 B G 1 1_555 B O2 C 64 B C 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 G 1 B G 1 1_555 B N4 C 64 B C 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 G 2 B G 2 1_555 B N3 C 63 B C 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 G 2 B G 2 1_555 B O2 C 63 B C 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 G 2 B G 2 1_555 B N4 C 63 B C 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 A 3 B A 3 1_555 B N3 U 62 B U 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N6 A 3 B A 3 1_555 B O4 U 62 B U 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 U 4 B U 4 1_555 B N1 A 61 B A 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O4 U 4 B U 4 1_555 B N6 A 61 B A 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 C 5 B C 5 1_555 B N1 G 60 B G 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 C 5 B C 5 1_555 B O6 G 60 B G 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 C 5 B C 5 1_555 B N2 G 60 B G 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 G 6 B G 6 1_555 B N3 C 59 B C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N2 G 6 B G 6 1_555 B O2 C 59 B C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O6 G 6 B G 6 1_555 B N4 C 59 B C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 A 7 B A 7 1_555 B N3 U 58 B U 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N6 A 7 B A 7 1_555 B O4 U 58 B U 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 U 8 B U 8 1_555 B N1 A 57 B A 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 U 8 B U 8 1_555 B N6 A 57 B A 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 C 9 B C 9 1_555 B N1 G 56 B G 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N4 C 9 B C 9 1_555 B O6 G 56 B G 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O2 C 9 B C 9 1_555 B N2 G 56 B G 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N1 G 10 B G 10 1_555 B N3 C 55 B C 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N2 G 10 B G 10 1_555 B O2 C 55 B C 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O6 G 10 B G 10 1_555 B N4 C 55 B C 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N1 A 11 B A 11 1_555 B N3 U 54 B U 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N6 A 11 B A 11 1_555 B O4 U 54 B U 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N3 U 12 B U 12 1_555 B N1 A 53 B A 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B O4 U 12 B U 12 1_555 B N6 A 53 B A 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N3 C 13 B C 13 1_555 B N1 G 52 B G 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B N4 C 13 B C 13 1_555 B O6 G 52 B G 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B O2 C 13 B C 13 1_555 B N2 G 52 B G 52 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 8DVS _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 5 106.726 122.475 90.339 1 50.71 ? PB ADP 1003 A 1 HETATM 2 O O1B ADP . . . E 5 105.758 122.335 89.191 1 50.71 ? O1B ADP 1003 A 1 HETATM 3 O O2B ADP . . . E 5 107.443 121.198 90.701 1 50.71 ? O2B ADP 1003 A 1 HETATM 4 O O3B ADP . . . E 5 106.181 123.238 91.52 1 50.71 ? O3B ADP 1003 A 1 HETATM 5 P PA ADP . . . E 5 108.574 123.179 88.336 1 50.71 ? PA ADP 1003 A 1 HETATM 6 O O1A ADP . . . E 5 109.632 124.236 88.13 1 50.71 ? O1A ADP 1003 A 1 HETATM 7 O O2A ADP . . . E 5 108.921 121.715 88.206 1 50.71 ? O2A ADP 1003 A 1 HETATM 8 O O3A ADP . . . E 5 107.899 123.423 89.778 1 50.71 ? O3A ADP 1003 A 1 HETATM 9 O O5' ADP . . . E 5 107.393 123.523 87.299 1 50.71 ? O5' ADP 1003 A 1 HETATM 10 C C5' ADP . . . E 5 106.803 124.821 87.322 1 50.71 ? C5' ADP 1003 A 1 HETATM 11 C C4' ADP . . . E 5 106.475 125.267 85.904 1 50.71 ? C4' ADP 1003 A 1 HETATM 12 O O4' ADP . . . E 5 106.468 126.695 85.854 1 50.71 ? O4' ADP 1003 A 1 HETATM 13 C C3' ADP . . . E 5 107.521 124.784 84.912 1 50.71 ? C3' ADP 1003 A 1 HETATM 14 O O3' ADP . . . E 5 106.943 123.834 84.012 1 50.71 ? O3' ADP 1003 A 1 HETATM 15 C C2' ADP . . . E 5 107.978 126.01 84.148 1 50.71 ? C2' ADP 1003 A 1 HETATM 16 O O2' ADP . . . E 5 107.681 125.861 82.757 1 50.71 ? O2' ADP 1003 A 1 HETATM 17 C C1' ADP . . . E 5 107.198 127.18 84.725 1 50.71 ? C1' ADP 1003 A 1 HETATM 18 N N9 ADP . . . E 5 108.145 128.238 85.157 1 50.71 ? N9 ADP 1003 A 1 HETATM 19 C C8 ADP . . . E 5 108.879 128.217 86.285 1 50.71 ? C8 ADP 1003 A 1 HETATM 20 N N7 ADP . . . E 5 109.649 129.331 86.391 1 50.71 ? N7 ADP 1003 A 1 HETATM 21 C C5 ADP . . . E 5 109.409 130.09 85.306 1 50.71 ? C5 ADP 1003 A 1 HETATM 22 C C6 ADP . . . E 5 109.887 131.394 84.791 1 50.71 ? C6 ADP 1003 A 1 HETATM 23 N N6 ADP . . . E 5 110.799 132.126 85.475 1 50.71 ? N6 ADP 1003 A 1 HETATM 24 N N1 ADP . . . E 5 109.383 131.828 83.615 1 50.71 ? N1 ADP 1003 A 1 HETATM 25 C C2 ADP . . . E 5 108.477 131.11 82.926 1 50.71 ? C2 ADP 1003 A 1 HETATM 26 N N3 ADP . . . E 5 107.999 129.921 83.333 1 50.71 ? N3 ADP 1003 A 1 HETATM 27 C C4 ADP . . . E 5 108.419 129.365 84.495 1 50.71 ? C4 ADP 1003 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #