data_5OOD # _model_server_result.job_id DMby4LAaKhbr-zUV7-0U8A _model_server_result.datetime_utc '2025-07-16 06:38:46' _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 5ood # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":401}' # _entry.id 5OOD # _exptl.entry_id 5OOD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 5 _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 5OOD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OOD _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 PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 ? 2 F N N ? 2 K N N ? 2 O N N ? 2 S N N ? 2 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 covale ? covale1 A C GLU 72 A GLU 72 1_555 A N HIC 73 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C HIC 73 A HIC 73 1_555 A N GLY 74 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 B C GLU 72 B GLU 72 1_555 B N HIC 73 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 B C HIC 73 B HIC 73 1_555 B N GLY 74 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 C C GLU 72 C GLU 72 1_555 C N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 C C HIC 73 C HIC 73 1_555 C N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale7 D C GLU 72 D GLU 72 1_555 D N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 D C HIC 73 D HIC 73 1_555 D N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale9 E C GLU 72 E GLU 72 1_555 E N HIC 73 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 E C HIC 73 E HIC 73 1_555 E N GLY 74 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 F O3B ADP . A ADP 401 1_555 I MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc2 G O3 PO4 . A PO4 402 1_555 I MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc3 K O3B ADP . B ADP 401 1_555 M MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc4 L O3 PO4 . B PO4 402 1_555 M MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc5 O O3B ADP . C ADP 401 1_555 Q MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc6 P O3 PO4 . C PO4 402 1_555 Q MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc7 S O3B ADP . D ADP 401 1_555 U MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc8 T O3 PO4 . D PO4 402 1_555 U MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc9 W O3B ADP . E ADP 401 1_555 Y MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc10 X O3 PO4 . E PO4 402 1_555 Y MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? # _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 104 n n PB O2B ADP sing 105 n n PB O3B ADP sing 106 n n PB O3A ADP sing 107 n n O2B HOB2 ADP sing 108 n n O3B HOB3 ADP sing 109 n n PA O1A ADP doub 110 n n PA O2A ADP sing 111 n n PA O3A ADP sing 112 n n PA O5' ADP sing 113 n n O2A HOA2 ADP sing 114 n n O5' C5' ADP sing 115 n n C5' C4' ADP sing 116 n n C5' "H5'1" ADP sing 117 n n C5' "H5'2" ADP sing 118 n n C4' O4' ADP sing 119 n n C4' C3' ADP sing 120 n n C4' H4' ADP sing 121 n n O4' C1' ADP sing 122 n n C3' O3' ADP sing 123 n n C3' C2' ADP sing 124 n n C3' H3' ADP sing 125 n n O3' HO3' ADP sing 126 n n C2' O2' ADP sing 127 n n C2' C1' ADP sing 128 n n C2' H2' ADP sing 129 n n O2' HO2' ADP sing 130 n n C1' N9 ADP sing 131 n n C1' H1' ADP sing 132 n n N9 C8 ADP sing 133 n y N9 C4 ADP sing 134 n y C8 N7 ADP doub 135 n y C8 H8 ADP sing 136 n n N7 C5 ADP sing 137 n y C5 C6 ADP sing 138 n y C5 C4 ADP doub 139 n y C6 N6 ADP sing 140 n n C6 N1 ADP doub 141 n y N6 HN61 ADP sing 142 n n N6 HN62 ADP sing 143 n n N1 C2 ADP sing 144 n y C2 N3 ADP doub 145 n y C2 H2 ADP sing 146 n n N3 C4 ADP sing 147 n y # _atom_sites.entry_id 5OOD _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 F 2 ADP A 1 401 376 ADP ADP . G 3 PO4 A 1 402 377 PO4 PO4 . H 4 9ZK A 1 403 378 9ZK 9ZK . I 5 MG A 1 404 379 MG MG . J 4 9ZK A 1 405 378 9ZK 9ZK . K 2 ADP B 1 401 376 ADP ADP . L 3 PO4 B 1 402 377 PO4 PO4 . M 5 MG B 1 403 379 MG MG . N 4 9ZK B 1 404 378 9ZK 9ZK . O 2 ADP C 1 401 376 ADP ADP . P 3 PO4 C 1 402 377 PO4 PO4 . Q 5 MG C 1 403 379 MG MG . R 4 9ZK C 1 404 378 9ZK 9ZK . S 2 ADP D 1 401 376 ADP ADP . T 3 PO4 D 1 402 377 PO4 PO4 . U 5 MG D 1 403 379 MG MG . V 4 9ZK D 1 404 378 9ZK 9ZK . W 2 ADP E 1 401 376 ADP ADP . X 3 PO4 E 1 402 377 PO4 PO4 . Y 5 MG E 1 403 379 MG MG . # 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 . . . S 2 144.149 168.504 111.249 1 31.44 ? PB ADP 401 D 1 HETATM 2 O O1B ADP . . . S 2 145.587 168.409 110.966 1 37.76 ? O1B ADP 401 D 1 HETATM 3 O O2B ADP . . . S 2 143.546 169.862 111.226 1 39.83 ? O2B ADP 401 D 1 HETATM 4 O O3B ADP . . . S 2 143.727 167.83 112.557 1 38.58 ? O3B ADP 401 D 1 HETATM 5 P PA ADP . . . S 2 142.233 166.991 110.477 1 34.82 ? PA ADP 401 D 1 HETATM 6 O O1A ADP . . . S 2 142.585 165.738 111.156 1 42.03 ? O1A ADP 401 D 1 HETATM 7 O O2A ADP . . . S 2 141.316 167.898 111.169 1 35.3 ? O2A ADP 401 D 1 HETATM 8 O O3A ADP . . . S 2 143.477 167.734 110.168 1 36.03 ? O3A ADP 401 D 1 HETATM 9 O O5' ADP . . . S 2 141.656 166.589 109.102 1 38.59 ? O5' ADP 401 D 1 HETATM 10 C C5' ADP . . . S 2 142.587 165.976 108.26 1 40.56 ? C5' ADP 401 D 1 HETATM 11 C C4' ADP . . . S 2 142.99 164.658 108.826 1 41.74 ? C4' ADP 401 D 1 HETATM 12 O O4' ADP . . . S 2 141.853 163.916 109.134 1 42.69 ? O4' ADP 401 D 1 HETATM 13 C C3' ADP . . . S 2 143.621 163.835 107.778 1 40.08 ? C3' ADP 401 D 1 HETATM 14 O O3' ADP . . . S 2 144.329 162.786 108.376 1 41.99 ? O3' ADP 401 D 1 HETATM 15 C C2' ADP . . . S 2 142.457 163.365 107.061 1 40.62 ? C2' ADP 401 D 1 HETATM 16 O O2' ADP . . . S 2 142.721 162.32 106.157 1 42.65 ? O2' ADP 401 D 1 HETATM 17 C C1' ADP . . . S 2 141.72 162.87 108.21 1 41.18 ? C1' ADP 401 D 1 HETATM 18 N N9 ADP . . . S 2 140.377 162.718 107.729 1 41.69 ? N9 ADP 401 D 1 HETATM 19 C C8 ADP . . . S 2 139.595 163.648 107.226 1 40.34 ? C8 ADP 401 D 1 HETATM 20 N N7 ADP . . . S 2 138.414 163.139 106.856 1 42.45 ? N7 ADP 401 D 1 HETATM 21 C C5 ADP . . . S 2 138.477 161.861 107.132 1 43.26 ? C5 ADP 401 D 1 HETATM 22 C C6 ADP . . . S 2 137.618 160.724 106.991 1 45.96 ? C6 ADP 401 D 1 HETATM 23 N N6 ADP . . . S 2 136.41 160.793 106.433 1 46.92 ? N6 ADP 401 D 1 HETATM 24 N N1 ADP . . . S 2 138.071 159.576 107.424 1 43.48 ? N1 ADP 401 D 1 HETATM 25 C C2 ADP . . . S 2 139.253 159.472 107.955 1 42.2 ? C2 ADP 401 D 1 HETATM 26 N N3 ADP . . . S 2 140.098 160.437 108.098 1 44.72 ? N3 ADP 401 D 1 HETATM 27 C C4 ADP . . . S 2 139.763 161.618 107.711 1 43.2 ? C4 ADP 401 D 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #