data_9B0U # _model_server_result.job_id 2PFmwdxFsEN9Qg4vUw7sVQ _model_server_result.datetime_utc '2025-03-02 23:45:56' _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 9b0u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":402}' # _entry.id 9B0U # _exptl.entry_id 9B0U _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 8 _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 9B0U _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9B0U _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA _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 ? 3 J N N ? 3 N N N ? 3 Q N N ? 3 V N N ? 3 Z N N ? 3 DA N N ? 3 HA N N ? 3 LA 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 J O3B ADP . A ADP 402 1_555 L MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc2 J O2A ADP . A ADP 402 1_555 L MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.71 ? metalc ? metalc3 K O4 PO4 . A PO4 403 1_555 L MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.845 ? metalc ? metalc4 N O3B ADP . B ADP 402 1_555 P MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc5 N O2A ADP . B ADP 402 1_555 P MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? metalc ? metalc6 O O3 PO4 . B PO4 403 1_555 P MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc7 Q O3B ADP . C ADP 401 1_555 T MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc8 Q O2A ADP . C ADP 401 1_555 T MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc9 R O1 PO4 . C PO4 402 1_555 T MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc10 V O3B ADP . D ADP 402 1_555 X MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc11 V O2A ADP . D ADP 402 1_555 X MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc12 W O3 PO4 . D PO4 403 1_555 X MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc13 Z O1B ADP . E ADP 402 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? metalc ? metalc14 Z O3B ADP . E ADP 402 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc15 Z O2A ADP . E ADP 402 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc16 AA O3 PO4 . E PO4 403 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? metalc ? metalc17 DA O3B ADP . F ADP 402 1_555 FA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc18 DA O2A ADP . F ADP 402 1_555 FA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.733 ? metalc ? metalc19 EA O3 PO4 . F PO4 403 1_555 FA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc20 HA O3B ADP . G ADP 402 1_555 JA MG MG . G MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? metalc ? metalc21 HA O2A ADP . G ADP 402 1_555 JA MG MG . G MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.702 ? metalc ? metalc22 IA O4 PO4 . G PO4 403 1_555 JA MG MG . G MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc23 LA O3B ADP . H ADP 402 1_555 NA MG MG . H MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc24 LA O2A ADP . H ADP 402 1_555 NA MG MG . H MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc25 MA O1 PO4 . H PO4 403 1_555 NA MG MG . H MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? # _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 9B0U _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 I 2 CRN A 1 401 401 CRN CRN . J 3 ADP A 1 402 402 ADP ADP . K 4 PO4 A 1 403 403 PO4 PO4 . L 5 MG A 1 404 1 MG MG . M 2 CRN B 1 401 401 CRN CRN . N 3 ADP B 1 402 402 ADP ADP . O 4 PO4 B 1 403 403 PO4 PO4 . P 5 MG B 1 404 2 MG MG . Q 3 ADP C 1 401 402 ADP ADP . R 4 PO4 C 1 402 403 PO4 PO4 . S 2 CRN C 1 403 404 CRN CRN . T 5 MG C 1 404 3 MG MG . U 2 CRN D 1 401 401 CRN CRN . V 3 ADP D 1 402 402 ADP ADP . W 4 PO4 D 1 403 403 PO4 PO4 . X 5 MG D 1 404 4 MG MG . Y 2 CRN E 1 401 401 CRN CRN . Z 3 ADP E 1 402 402 ADP ADP . AA 4 PO4 E 1 403 403 PO4 PO4 . BA 5 MG E 1 404 5 MG MG . CA 2 CRN F 1 401 401 CRN CRN . DA 3 ADP F 1 402 402 ADP ADP . EA 4 PO4 F 1 403 403 PO4 PO4 . FA 5 MG F 1 404 6 MG MG . GA 2 CRN G 1 401 401 CRN CRN . HA 3 ADP G 1 402 402 ADP ADP . IA 4 PO4 G 1 403 403 PO4 PO4 . JA 5 MG G 1 404 7 MG MG . KA 2 CRN H 1 401 401 CRN CRN . LA 3 ADP H 1 402 402 ADP ADP . MA 4 PO4 H 1 403 403 PO4 PO4 . NA 5 MG H 1 404 8 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 . . . V 3 92.726 147.361 120.119 1 155.95 ? PB ADP 402 D 1 HETATM 2 O O1B ADP . . . V 3 93.016 146.405 118.991 1 158.78 ? O1B ADP 402 D 1 HETATM 3 O O2B ADP . . . V 3 93.074 148.799 119.836 1 138.69 ? O2B ADP 402 D 1 HETATM 4 O O3B ADP . . . V 3 93.148 146.863 121.478 1 151.15 ? O3B ADP 402 D 1 HETATM 5 P PA ADP . . . V 3 90.426 146.4 121.298 1 144.26 ? PA ADP 402 D 1 HETATM 6 O O1A ADP . . . V 3 89.759 145.253 120.587 1 148.55 ? O1A ADP 402 D 1 HETATM 7 O O2A ADP . . . V 3 91.431 146.166 122.395 1 144.46 ? O2A ADP 402 D 1 HETATM 8 O O3A ADP . . . V 3 91.127 147.363 120.224 1 147.33 ? O3A ADP 402 D 1 HETATM 9 O O5' ADP . . . V 3 89.305 147.397 121.86 1 141.81 ? O5' ADP 402 D 1 HETATM 10 C C5' ADP . . . V 3 89.504 148.052 123.107 1 139.04 ? C5' ADP 402 D 1 HETATM 11 C C4' ADP . . . V 3 88.568 149.246 123.179 1 137.22 ? C4' ADP 402 D 1 HETATM 12 O O4' ADP . . . V 3 88.605 149.98 121.953 1 136.34 ? O4' ADP 402 D 1 HETATM 13 C C3' ADP . . . V 3 87.135 148.799 123.391 1 139.52 ? C3' ADP 402 D 1 HETATM 14 O O3' ADP . . . V 3 86.675 149.199 124.685 1 140.66 ? O3' ADP 402 D 1 HETATM 15 C C2' ADP . . . V 3 86.333 149.466 122.294 1 136.69 ? C2' ADP 402 D 1 HETATM 16 O O2' ADP . . . V 3 85.214 150.174 122.827 1 139.73 ? O2' ADP 402 D 1 HETATM 17 C C1' ADP . . . V 3 87.29 150.42 121.612 1 135.95 ? C1' ADP 402 D 1 HETATM 18 N N9 ADP . . . V 3 87.061 150.399 120.147 1 133.15 ? N9 ADP 402 D 1 HETATM 19 C C8 ADP . . . V 3 87.735 149.662 119.247 1 134.24 ? C8 ADP 402 D 1 HETATM 20 N N7 ADP . . . V 3 87.264 149.893 117.995 1 135.06 ? N7 ADP 402 D 1 HETATM 21 C C5 ADP . . . V 3 86.271 150.791 118.088 1 136.95 ? C5 ADP 402 D 1 HETATM 22 C C6 ADP . . . V 3 85.352 151.47 117.152 1 143.22 ? C6 ADP 402 D 1 HETATM 23 N N6 ADP . . . V 3 85.4 151.224 115.822 1 150.06 ? N6 ADP 402 D 1 HETATM 24 N N1 ADP . . . V 3 84.46 152.342 117.666 1 144.66 ? N1 ADP 402 D 1 HETATM 25 C C2 ADP . . . V 3 84.394 152.601 118.983 1 142.91 ? C2 ADP 402 D 1 HETATM 26 N N3 ADP . . . V 3 85.202 152.016 119.884 1 141.01 ? N3 ADP 402 D 1 HETATM 27 C C4 ADP . . . V 3 86.142 151.121 119.509 1 136.15 ? C4 ADP 402 D 1 HETATM 28 H "H5'1" ADP . . . V 3 89.296 147.363 123.928 1 141.35 ? "H5'1" ADP 402 D 1 HETATM 29 H "H5'2" ADP . . . V 3 90.54 148.386 123.191 1 139.13 ? "H5'2" ADP 402 D 1 HETATM 30 H H4' ADP . . . V 3 88.871 149.89 124.016 1 137.2 ? H4' ADP 402 D 1 HETATM 31 H H3' ADP . . . V 3 87.077 147.709 123.28 1 143.8 ? H3' ADP 402 D 1 HETATM 32 H HO3' ADP . . . V 3 85.838 148.757 124.884 1 143.84 ? HO3' ADP 402 D 1 HETATM 33 H H2' ADP . . . V 3 86.013 148.713 121.563 1 141.26 ? H2' ADP 402 D 1 HETATM 34 H HO2' ADP . . . V 3 84.616 149.551 123.256 1 143.15 ? HO2' ADP 402 D 1 HETATM 35 H H1' ADP . . . V 3 87.12 151.432 122.004 1 138.23 ? H1' ADP 402 D 1 HETATM 36 H H8 ADP . . . V 3 88.542 148.98 119.487 1 137.72 ? H8 ADP 402 D 1 HETATM 37 H HN61 ADP . . . V 3 84.763 151.697 115.198 1 149.98 ? HN61 ADP 402 D 1 HETATM 38 H HN62 ADP . . . V 3 86.074 150.567 115.455 1 148.07 ? HN62 ADP 402 D 1 HETATM 39 H H2 ADP . . . V 3 83.656 153.312 119.335 1 144.91 ? H2 ADP 402 D 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #