data_6D8C # _model_server_result.job_id AHfhAqyoDv7tR1GQzJ8KuQ _model_server_result.datetime_utc '2025-07-22 17:38:48' _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":"R","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 . . . R 4 131.808 154.892 123.754 1 46.14 ? PB ADP 401 K 1 HETATM 2 O O1B ADP . . . R 4 132.635 154.798 122.494 1 46.14 ? O1B ADP 401 K 1 HETATM 3 O O2B ADP . . . R 4 131.129 156.224 123.962 1 46.14 ? O2B ADP 401 K 1 HETATM 4 O O3B ADP . . . R 4 132.483 154.338 124.985 1 46.14 ? O3B ADP 401 K 1 HETATM 5 P PA ADP . . . R 4 129.522 154.2 122.328 1 46.14 ? PA ADP 401 K 1 HETATM 6 O O1A ADP . . . R 4 130.194 155.119 121.342 1 46.14 ? O1A ADP 401 K 1 HETATM 7 O O2A ADP . . . R 4 128.207 154.578 122.965 1 46.14 ? O2A ADP 401 K 1 HETATM 8 O O3A ADP . . . R 4 130.592 153.876 123.483 1 46.14 ? O3A ADP 401 K 1 HETATM 9 O O5' ADP . . . R 4 129.357 152.774 121.606 1 46.14 ? O5' ADP 401 K 1 HETATM 10 C C5' ADP . . . R 4 129.215 152.708 120.189 1 46.14 ? C5' ADP 401 K 1 HETATM 11 C C4' ADP . . . R 4 128.834 151.289 119.791 1 46.14 ? C4' ADP 401 K 1 HETATM 12 O O4' ADP . . . R 4 127.473 151.033 120.15 1 46.14 ? O4' ADP 401 K 1 HETATM 13 C C3' ADP . . . R 4 128.948 151.047 118.294 1 46.14 ? C3' ADP 401 K 1 HETATM 14 O O3' ADP . . . R 4 130.188 150.388 117.993 1 46.14 ? O3' ADP 401 K 1 HETATM 15 C C2' ADP . . . R 4 127.701 150.266 117.903 1 46.14 ? C2' ADP 401 K 1 HETATM 16 O O2' ADP . . . R 4 127.983 148.943 117.435 1 46.14 ? O2' ADP 401 K 1 HETATM 17 C C1' ADP . . . R 4 126.848 150.209 119.164 1 46.14 ? C1' ADP 401 K 1 HETATM 18 N N9 ADP . . . R 4 125.468 150.681 118.884 1 46.14 ? N9 ADP 401 K 1 HETATM 19 C C8 ADP . . . R 4 125.095 151.951 118.627 1 46.14 ? C8 ADP 401 K 1 HETATM 20 N N7 ADP . . . R 4 123.757 152.023 118.41 1 46.14 ? N7 ADP 401 K 1 HETATM 21 C C5 ADP . . . R 4 123.256 150.782 118.53 1 46.14 ? C5 ADP 401 K 1 HETATM 22 C C6 ADP . . . R 4 121.921 150.151 118.421 1 46.14 ? C6 ADP 401 K 1 HETATM 23 N N6 ADP . . . R 4 120.819 150.888 118.141 1 46.14 ? N6 ADP 401 K 1 HETATM 24 N N1 ADP . . . R 4 121.84 148.817 118.625 1 46.14 ? N1 ADP 401 K 1 HETATM 25 C C2 ADP . . . R 4 122.921 148.066 118.91 1 46.14 ? C2 ADP 401 K 1 HETATM 26 N N3 ADP . . . R 4 124.159 148.578 119.016 1 46.14 ? N3 ADP 401 K 1 HETATM 27 C C4 ADP . . . R 4 124.387 149.9 118.84 1 46.14 ? C4 ADP 401 K 1 HETATM 28 H "H5'1" ADP . . . R 4 130.155 152.988 119.71 1 46.14 ? "H5'1" ADP 401 K 1 HETATM 29 H "H5'2" ADP . . . R 4 128.443 153.407 119.862 1 46.14 ? "H5'2" ADP 401 K 1 HETATM 30 H H4' ADP . . . R 4 129.496 150.587 120.314 1 46.14 ? H4' ADP 401 K 1 HETATM 31 H H3' ADP . . . R 4 128.92 152.02 117.784 1 46.14 ? H3' ADP 401 K 1 HETATM 32 H HO3' ADP . . . R 4 130.282 150.298 117.035 1 46.14 ? HO3' ADP 401 K 1 HETATM 33 H H2' ADP . . . R 4 127.159 150.829 117.129 1 46.14 ? H2' ADP 401 K 1 HETATM 34 H HO2' ADP . . . R 4 128.484 148.99 116.61 1 46.14 ? HO2' ADP 401 K 1 HETATM 35 H H1' ADP . . . R 4 126.818 149.168 119.518 1 46.14 ? H1' ADP 401 K 1 HETATM 36 H H8 ADP . . . R 4 125.771 152.797 118.593 1 46.14 ? H8 ADP 401 K 1 HETATM 37 H HN61 ADP . . . R 4 119.917 150.44 118.074 1 46.14 ? HN61 ADP 401 K 1 HETATM 38 H HN62 ADP . . . R 4 120.901 151.884 117.996 1 46.14 ? HN62 ADP 401 K 1 HETATM 39 H H2 ADP . . . R 4 122.787 147.001 119.056 1 46.14 ? H2 ADP 401 K 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 63 _model_server_stats.query_time_ms 395 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #