data_7ZPR # _model_server_result.job_id Je-pYxyB1QJfAJar3u0teA _model_server_result.datetime_utc '2024-11-07 22:41:37' _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 7zpr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":1002}' # _entry.id 7ZPR # _exptl.entry_id 7ZPR _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 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 7ZPR _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZPR _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 dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 _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 O N N ? 4 Q N N ? 4 S N N ? 4 W N N ? 4 X N N ? 4 Z N N ? 4 BA 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 M MG MG . H MG 1001 1_555 N O3B ADP . H ADP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc2 O O3B ADP . D ADP 1001 1_555 P MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc3 Q O2B ADP . E ADP 301 1_555 R MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? metalc ? metalc4 Q O3B ADP . E ADP 301 1_555 R MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc5 Q O3A ADP . E ADP 301 1_555 R MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc6 S O3B ADP . F ADP 301 1_555 T MG MG . F MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc7 S O3A ADP . F ADP 301 1_555 T MG MG . F MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc8 E O VAL 49 I VAL 68 1_555 U K K . I K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.064 ? metalc ? metalc9 E O THR 50 I THR 69 1_555 U K K . I K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.977 ? metalc ? metalc10 E O ASN 164 I ASN 183 1_555 U K K . I K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc11 E O ALA 165 I ALA 184 1_555 U K K . I K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.055 ? metalc ? metalc12 E O THR 269 I THR 288 1_555 U K K . I K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc13 E O ALA 270 I ALA 289 1_555 U K K . I K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? metalc ? metalc14 E O THR 381 I THR 400 1_555 U K K . I K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? metalc ? metalc15 E O VAL 382 I VAL 401 1_555 U K K . I K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? metalc ? metalc16 V MG MG . A MG 1001 1_555 W O3B ADP . A ADP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? metalc ? metalc17 X O3B ADP . B ADP 1001 1_555 Y MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc18 X O1A ADP . B ADP 1001 1_555 Y MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc19 Z O2B ADP . J ADP 301 1_555 AA MG MG . J MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc20 BA O2B ADP . L ADP 301 1_555 CA MG MG . L MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc21 BA O2A ADP . L ADP 301 1_555 CA MG MG . L MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc22 J O VAL 49 M VAL 68 1_555 DA K K . M K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.015 ? metalc ? metalc23 J O THR 50 M THR 69 1_555 DA K K . M K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.046 ? metalc ? metalc24 J O ASN 164 M ASN 183 1_555 DA K K . M K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc25 J O ALA 165 M ALA 184 1_555 DA K K . M K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.136 ? metalc ? metalc26 J O THR 269 M THR 288 1_555 DA K K . M K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc27 J O ALA 270 M ALA 289 1_555 DA K K . M K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc28 J O THR 381 M THR 400 1_555 DA K K . M K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? metalc ? metalc29 J O VAL 382 M VAL 401 1_555 DA K K . M K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc30 K O VAL 49 C VAL 68 1_555 EA K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.064 ? metalc ? metalc31 K O THR 50 C THR 69 1_555 EA K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? metalc ? metalc32 K O ASN 164 C ASN 183 1_555 EA K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc33 K O ALA 165 C ALA 184 1_555 EA K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.057 ? metalc ? metalc34 K O THR 269 C THR 288 1_555 EA K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc35 K O ALA 270 C ALA 289 1_555 EA K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc36 K O THR 381 C THR 400 1_555 EA K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? metalc ? metalc37 K O VAL 382 C VAL 401 1_555 EA K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc38 L O VAL 49 G VAL 68 1_555 FA K K . G K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.014 ? metalc ? metalc39 L O THR 50 G THR 69 1_555 FA K K . G K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.046 ? metalc ? metalc40 L O ASN 164 G ASN 183 1_555 FA K K . G K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc41 L O ALA 165 G ALA 184 1_555 FA K K . G K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.136 ? metalc ? metalc42 L O THR 269 G THR 288 1_555 FA K K . G K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc43 L O ALA 270 G ALA 289 1_555 FA K K . G K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc44 L O THR 381 G THR 400 1_555 FA K K . G K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? metalc ? metalc45 L O VAL 382 G VAL 401 1_555 FA K K . G K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? # _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 7ZPR _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 M 3 MG H 1 1001 1001 MG MG . N 4 ADP H 1 1002 1002 ADP ADP . O 4 ADP D 1 1001 1001 ADP ADP . P 3 MG D 1 1002 1002 MG MG . Q 4 ADP E 1 301 301 ADP ADP . R 3 MG E 1 302 302 MG MG . S 4 ADP F 1 301 301 ADP ADP . T 3 MG F 1 302 302 MG MG . U 5 K I 1 601 601 K K . V 3 MG A 1 1001 1001 MG MG . W 4 ADP A 1 1002 1002 ADP ADP . X 4 ADP B 1 1001 1001 ADP ADP . Y 3 MG B 1 1002 1002 MG MG . Z 4 ADP J 1 301 301 ADP ADP . AA 3 MG J 1 302 302 MG MG . BA 4 ADP L 1 301 301 ADP ADP . CA 3 MG L 1 302 302 MG MG . DA 5 K M 1 501 501 K K . EA 5 K C 1 601 601 K K . FA 5 K G 1 501 501 K K . # 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 . . . W 4 137.808 139.177 116.8 1 38.61 ? PB ADP 1002 A 1 HETATM 2 O O1B ADP . . . W 4 137.184 139.808 115.583 1 38.61 ? O1B ADP 1002 A 1 HETATM 3 O O2B ADP . . . W 4 137.019 139.425 118.059 1 38.61 ? O2B ADP 1002 A 1 HETATM 4 O O3B ADP . . . W 4 139.271 139.521 116.957 1 38.61 ? O3B ADP 1002 A 1 HETATM 5 P PA ADP . . . W 4 138.731 136.421 117.08 1 38.61 ? PA ADP 1002 A 1 HETATM 6 O O1A ADP . . . W 4 138.02 135.114 116.973 1 38.61 ? O1A ADP 1002 A 1 HETATM 7 O O2A ADP . . . W 4 139.296 136.84 118.395 1 38.61 ? O2A ADP 1002 A 1 HETATM 8 O O3A ADP . . . W 4 137.756 137.582 116.563 1 38.61 ? O3A ADP 1002 A 1 HETATM 9 O O5' ADP . . . W 4 139.876 136.493 115.966 1 38.61 ? O5' ADP 1002 A 1 HETATM 10 C C5' ADP . . . W 4 140.536 135.276 115.553 1 38.61 ? C5' ADP 1002 A 1 HETATM 11 C C4' ADP . . . W 4 140.339 135.094 114.07 1 38.61 ? C4' ADP 1002 A 1 HETATM 12 O O4' ADP . . . W 4 141.03 133.89 113.647 1 38.61 ? O4' ADP 1002 A 1 HETATM 13 C C3' ADP . . . W 4 138.886 134.919 113.61 1 38.61 ? C3' ADP 1002 A 1 HETATM 14 O O3' ADP . . . W 4 138.68 135.561 112.36 1 38.61 ? O3' ADP 1002 A 1 HETATM 15 C C2' ADP . . . W 4 138.774 133.402 113.453 1 38.61 ? C2' ADP 1002 A 1 HETATM 16 O O2' ADP . . . W 4 137.736 133.011 112.581 1 38.61 ? O2' ADP 1002 A 1 HETATM 17 C C1' ADP . . . W 4 140.155 133.086 112.897 1 38.61 ? C1' ADP 1002 A 1 HETATM 18 N N9 ADP . . . W 4 140.549 131.694 113.063 1 38.61 ? N9 ADP 1002 A 1 HETATM 19 C C8 ADP . . . W 4 140.159 130.851 114.07 1 38.61 ? C8 ADP 1002 A 1 HETATM 20 N N7 ADP . . . W 4 140.662 129.647 113.963 1 38.61 ? N7 ADP 1002 A 1 HETATM 21 C C5 ADP . . . W 4 141.427 129.697 112.807 1 38.61 ? C5 ADP 1002 A 1 HETATM 22 C C6 ADP . . . W 4 142.21 128.731 112.151 1 38.61 ? C6 ADP 1002 A 1 HETATM 23 N N6 ADP . . . W 4 142.354 127.481 112.581 1 38.61 ? N6 ADP 1002 A 1 HETATM 24 N N1 ADP . . . W 4 142.844 129.106 111.016 1 38.61 ? N1 ADP 1002 A 1 HETATM 25 C C2 ADP . . . W 4 142.692 130.364 110.587 1 38.61 ? C2 ADP 1002 A 1 HETATM 26 N N3 ADP . . . W 4 141.982 131.354 111.12 1 38.61 ? N3 ADP 1002 A 1 HETATM 27 C C4 ADP . . . W 4 141.365 130.954 112.242 1 38.61 ? C4 ADP 1002 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #