data_6D8C # _model_server_result.job_id TzsOWdEXggnWmwtUAJZfjQ _model_server_result.datetime_utc '2025-07-22 11:05:07' _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 6d8c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":401}' # _entry.id 6D8C # _exptl.entry_id 6D8C _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 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 6D8C _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D8C _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 tridecameric _pdbx_struct_assembly.oligomeric_count 13 _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 N N N ? 4 P N N ? 4 R N N ? 4 T N N ? 4 V 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 K C HYP 1 N HYP 1 1_555 K N ALA 2 N ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 K N HYP 1 N HYP 1 1_555 K C CYS 7 N CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 K C TRP 3 N TRP 3 1_555 K N G5G 4 N G5G 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 K CD1 TRP 3 N TRP 3 1_555 K SG CYS 7 N CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? covale ? covale5 K C G5G 4 N G5G 4 1_555 K N ALA 5 N ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale6 K C ALA 5 N ALA 5 1_555 K N ALO 6 N ALO 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale7 K C ALO 6 N ALO 6 1_555 K N CYS 7 N CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale8 L C HYP 1 O HYP 1 1_555 L N ALA 2 O ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale9 L N HYP 1 O HYP 1 1_555 L C CYS 7 O CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 L C TRP 3 O TRP 3 1_555 L N G5G 4 O G5G 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 L CD1 TRP 3 O TRP 3 1_555 L SG CYS 7 O CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? covale ? covale12 L C G5G 4 O G5G 4 1_555 L N ALA 5 O ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale13 L C ALA 5 O ALA 5 1_555 L N ALO 6 O ALO 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale14 L C ALO 6 O ALO 6 1_555 L N CYS 7 O CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale15 M C HYP 1 P HYP 1 1_555 M N ALA 2 P ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale16 M N HYP 1 P HYP 1 1_555 M C CYS 7 P CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale17 M C TRP 3 P TRP 3 1_555 M N G5G 4 P G5G 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale18 M CD1 TRP 3 P TRP 3 1_555 M SG CYS 7 P CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? covale ? covale19 M C G5G 4 P G5G 4 1_555 M N ALA 5 P ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale20 M C ALA 5 P ALA 5 1_555 M N ALO 6 P ALO 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale21 M C ALO 6 P ALO 6 1_555 M N CYS 7 P CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 B OE1 GLN 137 H GLN 137 1_555 O MG MG . H MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc2 N O2B ADP . H ADP 401 1_555 O MG MG . H MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc3 N O3B ADP . H ADP 401 1_555 O MG MG . H MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc4 N O3A ADP . H ADP 401 1_555 O MG MG . H MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc5 D OE1 GLN 137 J GLN 137 1_555 Q MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc6 P O2B ADP . J ADP 401 1_555 Q MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc7 P O3B ADP . J ADP 401 1_555 Q MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc8 P O3A ADP . J ADP 401 1_555 Q MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc9 F OE1 GLN 137 K GLN 137 1_555 S MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc10 R O2B ADP . K ADP 401 1_555 S MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc11 R O3B ADP . K ADP 401 1_555 S MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc12 R O3A ADP . K ADP 401 1_555 S MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc13 H OE1 GLN 137 L GLN 137 1_555 U MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc14 T O2B ADP . L ADP 401 1_555 U MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc15 T O3B ADP . L ADP 401 1_555 U MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc16 T O3A ADP . L ADP 401 1_555 U MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc17 J OE1 GLN 137 M GLN 137 1_555 W MG MG . M MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc18 V O2B ADP . M ADP 401 1_555 W MG MG . M MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc19 V O3B ADP . M ADP 401 1_555 W MG MG . M MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc20 V O3A ADP . M ADP 401 1_555 W MG MG . M MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? # _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 6D8C _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 N 4 ADP H 1 401 401 ADP ADP . O 5 MG H 1 402 402 MG MG . P 4 ADP J 1 401 401 ADP ADP . Q 5 MG J 1 402 402 MG MG . R 4 ADP K 1 401 401 ADP ADP . S 5 MG K 1 402 402 MG MG . T 4 ADP L 1 401 401 ADP ADP . U 5 MG L 1 402 402 MG MG . V 4 ADP M 1 401 401 ADP ADP . W 5 MG M 1 402 402 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 . . . T 4 125.828 149.778 178.846 1 46.14 ? PB ADP 401 L 1 HETATM 2 O O1B ADP . . . T 4 126.609 150.064 177.584 1 46.14 ? O1B ADP 401 L 1 HETATM 3 O O2B ADP . . . T 4 124.623 150.663 179.053 1 46.14 ? O2B ADP 401 L 1 HETATM 4 O O3B ADP . . . T 4 126.681 149.588 180.076 1 46.14 ? O3B ADP 401 L 1 HETATM 5 P PA ADP . . . T 4 124.096 148.13 177.422 1 46.14 ? PA ADP 401 L 1 HETATM 6 O O1A ADP . . . T 4 124.284 149.254 176.435 1 46.14 ? O1A ADP 401 L 1 HETATM 7 O O2A ADP . . . T 4 122.752 147.878 178.059 1 46.14 ? O2A ADP 401 L 1 HETATM 8 O O3A ADP . . . T 4 125.198 148.324 178.576 1 46.14 ? O3A ADP 401 L 1 HETATM 9 O O5' ADP . . . T 4 124.59 146.782 176.701 1 46.14 ? O5' ADP 401 L 1 HETATM 10 C C5' ADP . . . T 4 124.493 146.658 175.285 1 46.14 ? C5' ADP 401 L 1 HETATM 11 C C4' ADP . . . T 4 124.789 145.22 174.888 1 46.14 ? C4' ADP 401 L 1 HETATM 12 O O4' ADP . . . T 4 123.69 144.379 175.247 1 46.14 ? O4' ADP 401 L 1 HETATM 13 C C3' ADP . . . T 4 125 145.053 173.39 1 46.14 ? C3' ADP 401 L 1 HETATM 14 O O3' ADP . . . T 4 126.403 145.02 173.089 1 46.14 ? O3' ADP 401 L 1 HETATM 15 C C2' ADP . . . T 4 124.237 143.794 173 1 46.14 ? C2' ADP 401 L 1 HETATM 16 O O2' ADP . . . T 4 125.083 142.738 172.535 1 46.14 ? O2' ADP 401 L 1 HETATM 17 C C1' ADP . . . T 4 123.501 143.36 174.263 1 46.14 ? C1' ADP 401 L 1 HETATM 18 N N9 ADP . . . T 4 122.055 143.161 173.983 1 46.14 ? N9 ADP 401 L 1 HETATM 19 C C8 ADP . . . T 4 121.152 144.128 173.725 1 46.14 ? C8 ADP 401 L 1 HETATM 20 N N7 ADP . . . T 4 119.924 143.592 173.509 1 46.14 ? N7 ADP 401 L 1 HETATM 21 C C5 ADP . . . T 4 120.034 142.258 173.63 1 46.14 ? C5 ADP 401 L 1 HETATM 22 C C6 ADP . . . T 4 119.125 141.095 173.524 1 46.14 ? C6 ADP 401 L 1 HETATM 23 N N6 ADP . . . T 4 117.809 141.257 173.243 1 46.14 ? N6 ADP 401 L 1 HETATM 24 N N1 ADP . . . T 4 119.653 139.866 173.728 1 46.14 ? N1 ADP 401 L 1 HETATM 25 C C2 ADP . . . T 4 120.956 139.68 174.014 1 46.14 ? C2 ADP 401 L 1 HETATM 26 N N3 ADP . . . T 4 121.831 140.695 174.118 1 46.14 ? N3 ADP 401 L 1 HETATM 27 C C4 ADP . . . T 4 121.441 141.979 173.941 1 46.14 ? C4 ADP 401 L 1 HETATM 28 H "H5'1" ADP . . . T 4 125.206 147.33 174.804 1 46.14 ? "H5'1" ADP 401 L 1 HETATM 29 H "H5'2" ADP . . . T 4 123.488 146.934 174.956 1 46.14 ? "H5'2" ADP 401 L 1 HETATM 30 H H4' ADP . . . T 4 125.697 144.889 175.41 1 46.14 ? H4' ADP 401 L 1 HETATM 31 H H3' ADP . . . T 4 124.537 145.908 172.88 1 46.14 ? H3' ADP 401 L 1 HETATM 32 H HO3' ADP . . . T 4 126.527 144.981 172.131 1 46.14 ? HO3' ADP 401 L 1 HETATM 33 H H2' ADP . . . T 4 123.499 144.051 172.227 1 46.14 ? H2' ADP 401 L 1 HETATM 34 H HO2' ADP . . . T 4 125.509 143.005 171.709 1 46.14 ? HO2' ADP 401 L 1 HETATM 35 H H1' ADP . . . T 4 123.941 142.418 174.617 1 46.14 ? H1' ADP 401 L 1 HETATM 36 H H8 ADP . . . T 4 121.376 145.188 173.691 1 46.14 ? H8 ADP 401 L 1 HETATM 37 H HN61 ADP . . . T 4 117.205 140.451 173.177 1 46.14 ? HN61 ADP 401 L 1 HETATM 38 H HN62 ADP . . . T 4 117.435 142.184 173.098 1 46.14 ? HN62 ADP 401 L 1 HETATM 39 H H2 ADP . . . T 4 121.315 138.67 174.16 1 46.14 ? H2 ADP 401 L 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 68 _model_server_stats.query_time_ms 431 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 39 #