data_6DUQ # _model_server_result.job_id DidHGOWGdg_oCvLHfjMWqg _model_server_result.datetime_utc '2024-11-12 21:24:47' _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 6duq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"VA","auth_seq_id":1000}' # _entry.id 6DUQ # _exptl.entry_id 6DUQ _exptl.method 'X-RAY DIFFRACTION' # _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 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 89.94 _cell.angle_beta 89.9 _cell.angle_gamma 60.01 _cell.entry_id 6DUQ _cell.length_a 126.35 _cell.length_b 126.32 _cell.length_c 166.82 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DUQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tridecameric 13 author_defined_assembly 1 ? tridecameric 13 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,G,I,K,P,Q,R,V,W,X,Z,AA,BA,CA,GA,HA,IA,MA,NA,OA,SA,TA,UA,YA,ZA,AB,EB,FB,GB 1 1 B,D,F,H,J,L,M,N,O,S,T,U,Y,DA,EA,FA,JA,KA,LA,PA,QA,RA,VA,WA,XA,BB,CB,DB,HB,IB,JB 2 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 x,y,z _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 AA N N ? 4 DA N N ? 4 GA N N ? 4 JA N N ? 4 MA N N ? 4 PA N N ? 4 SA N N ? 4 VA N N ? 4 YA N N ? 4 BB N N ? 4 EB N N ? 4 HB 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 metalc ? metalc1 A OG1 THR 188 L THR 185 1_555 BA MG MG . L MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc2 AA O1B ADP . L ADP 1000 1_555 BA MG MG . L MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc3 AA O2B ADP . L ADP 1000 1_555 CA BE BEF . L BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.737 ? metalc ? metalc4 B OG1 THR 188 A THR 185 1_555 EA MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc5 DA O1B ADP . A ADP 1000 1_555 EA MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc6 DA O2B ADP . A ADP 1000 1_555 FA BE BEF . A BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? metalc ? metalc7 C OG1 THR 188 G THR 185 1_555 HA MG MG . G MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc8 GA O1B ADP . G ADP 1000 1_555 HA MG MG . G MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc9 GA O2B ADP . G ADP 1000 1_555 IA BE BEF . G BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? metalc ? metalc10 D OG1 THR 188 B THR 185 1_555 KA MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc11 JA O1B ADP . B ADP 1000 1_555 KA MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc12 JA O2B ADP . B ADP 1000 1_555 LA BE BEF . B BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.715 ? metalc ? metalc13 E OG1 THR 188 H THR 185 1_555 NA MG MG . H MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc14 MA O1B ADP . H ADP 1000 1_555 NA MG MG . H MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc15 MA O2B ADP . H ADP 1000 1_555 OA BE BEF . H BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.728 ? metalc ? metalc16 F OG1 THR 188 C THR 185 1_555 QA MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc17 PA O1B ADP . C ADP 1000 1_555 QA MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc18 PA O2B ADP . C ADP 1000 1_555 RA BE BEF . C BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.749 ? metalc ? metalc19 G OG1 THR 188 I THR 185 1_555 TA MG MG . I MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc20 SA O1B ADP . I ADP 1000 1_555 TA MG MG . I MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc21 SA O2B ADP . I ADP 1000 1_555 UA BE BEF . I BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.762 ? metalc ? metalc22 H OG1 THR 188 D THR 185 1_555 WA MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc23 VA O1B ADP . D ADP 1000 1_555 WA MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc24 VA O2B ADP . D ADP 1000 1_555 XA BE BEF . D BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.734 ? metalc ? metalc25 I OG1 THR 188 K THR 185 1_555 ZA MG MG . K MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc26 YA O1B ADP . K ADP 1000 1_555 ZA MG MG . K MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc27 YA O2B ADP . K ADP 1000 1_555 AB BE BEF . K BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.749 ? metalc ? metalc28 J OG1 THR 188 F THR 185 1_555 CB MG MG . F MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc29 BB O1B ADP . F ADP 1000 1_555 CB MG MG . F MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc30 BB O2B ADP . F ADP 1000 1_555 DB BE BEF . F BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 ? metalc ? metalc31 K OG1 THR 188 J THR 185 1_555 FB MG MG . J MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc32 EB O1B ADP . J ADP 1000 1_555 FB MG MG . J MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc33 EB O2B ADP . J ADP 1000 1_555 GB BE BEF . J BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.741 ? metalc ? metalc34 L OG1 THR 188 E THR 185 1_555 IB MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc35 HB O1B ADP . E ADP 1000 1_555 IB MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc36 HB O2B ADP . E ADP 1000 1_555 JB BE BEF . E BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? # _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 6DUQ _atom_sites.fract_transf_matrix[1][1] 0.007915 _atom_sites.fract_transf_matrix[1][2] -0.004567 _atom_sites.fract_transf_matrix[1][3] -0.000013 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00914 _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] 0.005994 _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 AA 4 ADP L 1 1000 1000 ADP ADP . BA 5 MG L 1 1001 1001 MG MG . CA 6 BEF L 1 1002 1002 BEF BEF . DA 4 ADP A 1 1000 1000 ADP ADP . EA 5 MG A 1 1001 1001 MG MG . FA 6 BEF A 1 1002 1002 BEF BEF . GA 4 ADP G 1 1000 1000 ADP ADP . HA 5 MG G 1 1001 1001 MG MG . IA 6 BEF G 1 1002 1002 BEF BEF . JA 4 ADP B 1 1000 1000 ADP ADP . KA 5 MG B 1 1001 1001 MG MG . LA 6 BEF B 1 1002 1002 BEF BEF . MA 4 ADP H 1 1000 1000 ADP ADP . NA 5 MG H 1 1001 1001 MG MG . OA 6 BEF H 1 1002 1002 BEF BEF . PA 4 ADP C 1 1000 1000 ADP ADP . QA 5 MG C 1 1001 1001 MG MG . RA 6 BEF C 1 1002 1002 BEF BEF . SA 4 ADP I 1 1000 1000 ADP ADP . TA 5 MG I 1 1001 1001 MG MG . UA 6 BEF I 1 1002 1002 BEF BEF . VA 4 ADP D 1 1000 1000 ADP ADP . WA 5 MG D 1 1001 1001 MG MG . XA 6 BEF D 1 1002 1002 BEF BEF . YA 4 ADP K 1 1000 1000 ADP ADP . ZA 5 MG K 1 1001 1001 MG MG . AB 6 BEF K 1 1002 1002 BEF BEF . BB 4 ADP F 1 1000 1000 ADP ADP . CB 5 MG F 1 1001 1001 MG MG . DB 6 BEF F 1 1002 1002 BEF BEF . EB 4 ADP J 1 1000 1000 ADP ADP . FB 5 MG J 1 1001 1001 MG MG . GB 6 BEF J 1 1002 1002 BEF BEF . HB 4 ADP E 1 1000 1000 ADP ADP . IB 5 MG E 1 1001 1001 MG MG . JB 6 BEF E 1 1002 1002 BEF BEF . # 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 . . . VA 4 -40.315 15.05 70.116 1 132.43 ? PB ADP 1000 D 1 HETATM 2 O O1B ADP . . . VA 4 -39.088 14.68 69.325 1 134.36 ? O1B ADP 1000 D 1 HETATM 3 O O2B ADP . . . VA 4 -41.176 16.123 69.489 1 132.43 ? O2B ADP 1000 D 1 HETATM 4 O O3B ADP . . . VA 4 -41.061 13.861 70.664 1 137.3 ? O3B ADP 1000 D 1 HETATM 5 P PA ADP . . . VA 4 -38.316 16.529 71.436 1 150.82 ? PA ADP 1000 D 1 HETATM 6 O O1A ADP . . . VA 4 -38.369 17.498 70.279 1 132.43 ? O1A ADP 1000 D 1 HETATM 7 O O2A ADP . . . VA 4 -37.191 15.535 71.611 1 132.43 ? O2A ADP 1000 D 1 HETATM 8 O O3A ADP . . . VA 4 -39.711 15.728 71.442 1 147.59 ? O3A ADP 1000 D 1 HETATM 9 O O5' ADP . . . VA 4 -38.429 17.396 72.787 1 181.76 ? O5' ADP 1000 D 1 HETATM 10 C C5' ADP . . . VA 4 -39.124 18.642 72.767 1 157.2 ? C5' ADP 1000 D 1 HETATM 11 C C4' ADP . . . VA 4 -38.71 19.471 73.971 1 137.68 ? C4' ADP 1000 D 1 HETATM 12 O O4' ADP . . . VA 4 -38.704 18.69 75.165 1 144.76 ? O4' ADP 1000 D 1 HETATM 13 C C3' ADP . . . VA 4 -37.287 19.958 73.812 1 139.92 ? C3' ADP 1000 D 1 HETATM 14 O O3' ADP . . . VA 4 -37.294 21.239 73.186 1 163.3 ? O3' ADP 1000 D 1 HETATM 15 C C2' ADP . . . VA 4 -36.739 20.026 75.22 1 132.69 ? C2' ADP 1000 D 1 HETATM 16 O O2' ADP . . . VA 4 -36.889 21.345 75.751 1 144.7 ? O2' ADP 1000 D 1 HETATM 17 C C1' ADP . . . VA 4 -37.617 19.078 76.007 1 132.43 ? C1' ADP 1000 D 1 HETATM 18 N N9 ADP . . . VA 4 -36.785 17.899 76.294 1 132.43 ? N9 ADP 1000 D 1 HETATM 19 C C8 ADP . . . VA 4 -36.833 16.721 75.655 1 132.43 ? C8 ADP 1000 D 1 HETATM 20 N N7 ADP . . . VA 4 -35.921 15.865 76.176 1 132.43 ? N7 ADP 1000 D 1 HETATM 21 C C5 ADP . . . VA 4 -35.269 16.504 77.166 1 132.43 ? C5 ADP 1000 D 1 HETATM 22 C C6 ADP . . . VA 4 -34.185 16.189 78.132 1 132.43 ? C6 ADP 1000 D 1 HETATM 23 N N6 ADP . . . VA 4 -33.581 14.976 78.159 1 132.43 ? N6 ADP 1000 D 1 HETATM 24 N N1 ADP . . . VA 4 -33.813 17.16 78.995 1 132.43 ? N1 ADP 1000 D 1 HETATM 25 C C2 ADP . . . VA 4 -34.394 18.373 78.992 1 133.03 ? C2 ADP 1000 D 1 HETATM 26 N N3 ADP . . . VA 4 -35.378 18.726 78.148 1 132.43 ? N3 ADP 1000 D 1 HETATM 27 C C4 ADP . . . VA 4 -35.849 17.85 77.233 1 132.43 ? C4 ADP 1000 D 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 60 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #