data_5I0I # _model_server_result.job_id yGO3LakUEgU0wnG5gTRpAg _model_server_result.datetime_utc '2025-02-05 08:45:24' _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 5i0i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":904}' # _entry.id 5I0I # _exptl.entry_id 5I0I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 5I0I _cell.length_a 113.95 _cell.length_b 173.41 _cell.length_c 178.75 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5I0I _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 software_defined_assembly 1 PISA trimeric 3 software_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,H,I,J,K,L,M,N,O,U,W 1 1 B,D,F,P,Q,R,S,T,V,X 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 ? 9 J N N ? 9 R 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 162 A THR 164 1_555 H MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc2 A OG SER 217 A SER 219 1_555 H MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc3 H MG MG . A MG 902 1_555 I O1 VO4 . A VO4 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc4 H MG MG . A MG 902 1_555 J O1B ADP . A ADP 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc5 H MG MG . A MG 902 1_555 W O HOH . A HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc6 H MG MG . A MG 902 1_555 W O HOH . A HOH 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc7 I V VO4 . A VO4 903 1_555 J O3B ADP . A ADP 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc8 B OG1 THR 162 B THR 164 1_555 Q MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc9 B OG SER 217 B SER 219 1_555 Q MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc10 Q MG MG . B MG 902 1_555 R O2B ADP . B ADP 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc11 Q MG MG . B MG 902 1_555 S O1 VO4 . B VO4 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc12 Q MG MG . B MG 902 1_555 X O HOH . B HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc13 Q MG MG . B MG 902 1_555 X O HOH . B HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc14 R O3B ADP . B ADP 903 1_555 S V VO4 . B VO4 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? # _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 5I0I _atom_sites.fract_transf_matrix[1][1] 0.008776 _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] 0.005767 _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] 0.005594 _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 G 6 MPO A 1 901 1 MPO MPO . H 7 MG A 1 902 1 MG MG . I 8 VO4 A 1 903 998 VO4 VO4 . J 9 ADP A 1 904 999 ADP ADP . K 10 SO4 A 1 905 2 SO4 SO4 . L 10 SO4 A 1 906 5 SO4 SO4 . M 10 SO4 A 1 907 6 SO4 SO4 . N 10 SO4 A 1 908 7 SO4 SO4 . O 10 SO4 A 1 909 8 SO4 SO4 . P 6 MPO B 1 901 2 MPO MPO . Q 7 MG B 1 902 2 MG MG . R 9 ADP B 1 903 999 ADP ADP . S 8 VO4 B 1 904 998 VO4 VO4 . T 10 SO4 B 1 905 3 SO4 SO4 . U 10 SO4 C 1 201 1 SO4 SO4 . V 10 SO4 E 1 201 4 SO4 SO4 . W 11 HOH A 1 1001 2 HOH HOH . W 11 HOH A 2 1002 11 HOH HOH . W 11 HOH A 3 1003 27 HOH HOH . W 11 HOH A 4 1004 24 HOH HOH . W 11 HOH A 5 1005 14 HOH HOH . W 11 HOH A 6 1006 1 HOH HOH . W 11 HOH A 7 1007 32 HOH HOH . W 11 HOH A 8 1008 12 HOH HOH . W 11 HOH A 9 1009 23 HOH HOH . W 11 HOH A 10 1010 33 HOH HOH . W 11 HOH A 11 1011 30 HOH HOH . X 11 HOH B 1 1001 31 HOH HOH . X 11 HOH B 2 1002 6 HOH HOH . X 11 HOH B 3 1003 3 HOH HOH . X 11 HOH B 4 1004 26 HOH HOH . X 11 HOH B 5 1005 29 HOH HOH . # 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 . . . J 9 -20.909 -36.326 5.304 1 79.35 ? PB ADP 904 A 1 HETATM 2 O O1B ADP . . . J 9 -21.095 -35.309 4.256 1 79.8 ? O1B ADP 904 A 1 HETATM 3 O O2B ADP . . . J 9 -19.687 -36.084 6.229 1 78.21 ? O2B ADP 904 A 1 HETATM 4 O O3B ADP . . . J 9 -20.783 -37.67 4.845 1 78.55 ? O3B ADP 904 A 1 HETATM 5 P PA ADP . . . J 9 -23.427 -35.545 6.417 1 71.36 ? PA ADP 904 A 1 HETATM 6 O O1A ADP . . . J 9 -24.619 -35.724 5.45 1 73.41 ? O1A ADP 904 A 1 HETATM 7 O O2A ADP . . . J 9 -22.888 -34.171 6.413 1 70.58 ? O2A ADP 904 A 1 HETATM 8 O O3A ADP . . . J 9 -22.263 -36.568 6.098 1 74.16 ? O3A ADP 904 A 1 HETATM 9 O O5' ADP . . . J 9 -23.795 -35.997 7.862 1 69.32 ? O5' ADP 904 A 1 HETATM 10 C C5' ADP . . . J 9 -24.359 -37.294 8.11 1 71.56 ? C5' ADP 904 A 1 HETATM 11 C C4' ADP . . . J 9 -25.69 -37.144 8.8 1 74.74 ? C4' ADP 904 A 1 HETATM 12 O O4' ADP . . . J 9 -25.479 -36.982 10.223 1 72.84 ? O4' ADP 904 A 1 HETATM 13 C C3' ADP . . . J 9 -26.508 -35.927 8.374 1 78.64 ? C3' ADP 904 A 1 HETATM 14 O O3' ADP . . . J 9 -27.128 -35.952 7.084 1 81.69 ? O3' ADP 904 A 1 HETATM 15 C C2' ADP . . . J 9 -27.352 -35.663 9.616 1 76.24 ? C2' ADP 904 A 1 HETATM 16 O O2' ADP . . . J 9 -28.458 -36.548 9.677 1 76.06 ? O2' ADP 904 A 1 HETATM 17 C C1' ADP . . . J 9 -26.34 -35.978 10.727 1 75.9 ? C1' ADP 904 A 1 HETATM 18 N N9 ADP . . . J 9 -25.529 -34.83 11.124 1 77.72 ? N9 ADP 904 A 1 HETATM 19 C C8 ADP . . . J 9 -24.343 -34.426 10.566 1 80.35 ? C8 ADP 904 A 1 HETATM 20 N N7 ADP . . . J 9 -23.909 -33.271 11.012 1 83.44 ? N7 ADP 904 A 1 HETATM 21 C C5 ADP . . . J 9 -24.863 -32.9 11.944 1 82.69 ? C5 ADP 904 A 1 HETATM 22 C C6 ADP . . . J 9 -24.97 -31.782 12.792 1 83.9 ? C6 ADP 904 A 1 HETATM 23 N N6 ADP . . . J 9 -24.16 -30.728 12.72 1 82.96 ? N6 ADP 904 A 1 HETATM 24 N N1 ADP . . . J 9 -26.008 -31.749 13.66 1 86.27 ? N1 ADP 904 A 1 HETATM 25 C C2 ADP . . . J 9 -26.901 -32.747 13.636 1 87.23 ? C2 ADP 904 A 1 HETATM 26 N N3 ADP . . . J 9 -26.922 -33.834 12.856 1 85.1 ? N3 ADP 904 A 1 HETATM 27 C C4 ADP . . . J 9 -25.861 -33.856 12.033 1 81.04 ? C4 ADP 904 A 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #