data_1SXJ # _model_server_result.job_id jlCQ3x1H9uoSIwtvOc47dw _model_server_result.datetime_utc '2025-07-31 04:23:02' _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 1sxj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":805}' # _entry.id 1SXJ # _exptl.entry_id 1SXJ _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 1 _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 1SXJ _cell.length_a 104.209 _cell.length_b 110.481 _cell.length_c 268.206 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SXJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_and_software_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 _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 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 # _struct_asym.details ? _struct_asym.entity_id 9 _struct_asym.id Q _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 F C SER 25 F SER 0 1_555 F N MSE 26 F MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 F C MSE 26 F MSE 1 1_555 F N LEU 27 F LEU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 F C GLY 94 F GLY 69 1_555 F N MSE 95 F MSE 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 F C MSE 95 F MSE 70 1_555 F N ASP 96 F ASP 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 F C LEU 143 F LEU 118 1_555 F N MSE 144 F MSE 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 F C MSE 144 F MSE 119 1_555 F N ASP 145 F ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 F C ILE 185 F ILE 160 1_555 F N MSE 186 F MSE 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale8 F C MSE 186 F MSE 161 1_555 F N ILE 187 F ILE 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 F C ASP 212 F ASP 187 1_555 F N MSE 213 F MSE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale10 F C MSE 213 F MSE 188 1_555 F N GLU 214 F GLU 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 F C GLU 223 F GLU 198 1_555 F N MSE 224 F MSE 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 F C MSE 224 F MSE 199 1_555 F N ASP 225 F ASP 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale13 G C MSE 23 G MSE -2 1_555 G N ALA 24 G ALA -1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale14 G C SER 25 G SER 0 1_555 G N MSE 26 G MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 G C MSE 26 G MSE 1 1_555 G N LEU 27 G LEU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale16 G C GLY 94 G GLY 69 1_555 G N MSE 95 G MSE 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale17 G C MSE 95 G MSE 70 1_555 G N ASP 96 G ASP 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale18 G C LEU 143 G LEU 118 1_555 G N MSE 144 G MSE 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale19 G C MSE 144 G MSE 119 1_555 G N ASP 145 G ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale20 G C ILE 185 G ILE 160 1_555 G N MSE 186 G MSE 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale21 G C MSE 186 G MSE 161 1_555 G N ILE 187 G ILE 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale22 G C ASP 212 G ASP 187 1_555 G N MSE 213 G MSE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale23 G C MSE 213 G MSE 188 1_555 G N GLU 214 G GLU 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale24 G C GLU 223 G GLU 198 1_555 G N MSE 224 G MSE 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale25 G C MSE 224 G MSE 199 1_555 G N ASP 225 G ASP 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale26 H C HIS 22 H HIS -3 1_555 H N MSE 23 H MSE -2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale27 H C MSE 23 H MSE -2 1_555 H N ALA 24 H ALA -1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale28 H C SER 25 H SER 0 1_555 H N MSE 26 H MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale29 H C MSE 26 H MSE 1 1_555 H N LEU 27 H LEU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale30 H C GLY 94 H GLY 69 1_555 H N MSE 95 H MSE 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale31 H C MSE 95 H MSE 70 1_555 H N ASP 96 H ASP 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale32 H C LEU 143 H LEU 118 1_555 H N MSE 144 H MSE 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale33 H C MSE 144 H MSE 119 1_555 H N ASP 145 H ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale34 H C ILE 185 H ILE 160 1_555 H N MSE 186 H MSE 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale35 H C MSE 186 H MSE 161 1_555 H N ILE 187 H ILE 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale36 H C ASP 212 H ASP 187 1_555 H N MSE 213 H MSE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale37 H C MSE 213 H MSE 188 1_555 H N GLU 214 H GLU 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale38 H C GLU 223 H GLU 198 1_555 H N MSE 224 H MSE 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale39 H C MSE 224 H MSE 199 1_555 H N ASP 225 H ASP 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OG1 THR 91 A THR 360 1_555 I MG MG . A MG 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc2 J O1B AGS . A AGS 801 1_555 I MG MG . A MG 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc3 J O3G AGS . A AGS 801 1_555 I MG MG . A MG 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc4 B OG1 THR 56 B THR 56 1_555 K MG MG . B MG 812 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.813 ? metalc ? metalc5 L O3G AGS . B AGS 802 1_555 K MG MG . B MG 812 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc6 L O1B AGS . B AGS 802 1_555 K MG MG . B MG 812 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc7 C OG1 THR 60 C THR 60 1_555 M MG MG . C MG 813 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc8 N O1B AGS . C AGS 803 1_555 M MG MG . C MG 813 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc9 N O3G AGS . C AGS 803 1_555 M MG MG . C MG 813 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc10 D OG1 THR 72 D THR 72 1_555 O MG MG . D MG 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc11 P O2B AGS . D AGS 804 1_555 O MG MG . D MG 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc12 P O3G AGS . D AGS 804 1_555 O MG MG . D MG 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? # _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 1SXJ _atom_sites.fract_transf_matrix[1][1] 0.009596 _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] 0.009051 _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] 0.003728 _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 7 MG A 1 811 811 MG MG . J 8 AGS A 1 801 801 AGS ATG . K 7 MG B 1 812 812 MG MG . L 8 AGS B 1 802 802 AGS ATG . M 7 MG C 1 813 813 MG MG . N 8 AGS C 1 803 803 AGS ATG . O 7 MG D 1 814 814 MG MG . P 8 AGS D 1 804 804 AGS ATG . Q 9 ADP E 1 805 805 ADP ADP . # 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 . . . Q 9 27.974 18.736 22.118 1 93.12 ? PB ADP 805 E 1 HETATM 2 O O1B ADP . . . Q 9 26.779 17.904 21.644 1 93.12 ? O1B ADP 805 E 1 HETATM 3 O O2B ADP . . . Q 9 28.017 20.131 21.678 1 93.12 ? O2B ADP 805 E 1 HETATM 4 O O3B ADP . . . Q 9 28.052 18.758 23.686 1 93.12 ? O3B ADP 805 E 1 HETATM 5 P PA ADP . . . Q 9 30.82 18.471 21.998 1 93.12 ? PA ADP 805 E 1 HETATM 6 O O1A ADP . . . Q 9 31.47 18.513 20.654 1 93.12 ? O1A ADP 805 E 1 HETATM 7 O O2A ADP . . . Q 9 30.939 19.759 22.763 1 93.12 ? O2A ADP 805 E 1 HETATM 8 O O3A ADP . . . Q 9 29.288 18.066 21.75 1 93.12 ? O3A ADP 805 E 1 HETATM 9 O O5' ADP . . . Q 9 31.35 17.189 22.839 1 93.12 ? O5' ADP 805 E 1 HETATM 10 C C5' ADP . . . Q 9 32.679 17.386 23.45 1 93.12 ? C5' ADP 805 E 1 HETATM 11 C C4' ADP . . . Q 9 33.584 16.131 23.524 1 93.12 ? C4' ADP 805 E 1 HETATM 12 O O4' ADP . . . Q 9 32.964 15.006 22.802 1 93.12 ? O4' ADP 805 E 1 HETATM 13 C C3' ADP . . . Q 9 34.978 16.234 22.871 1 93.12 ? C3' ADP 805 E 1 HETATM 14 O O3' ADP . . . Q 9 35.936 16.94 23.635 1 93.12 ? O3' ADP 805 E 1 HETATM 15 C C2' ADP . . . Q 9 35.305 14.76 22.585 1 93.12 ? C2' ADP 805 E 1 HETATM 16 O O2' ADP . . . Q 9 35.976 14.059 23.619 1 93.12 ? O2' ADP 805 E 1 HETATM 17 C C1' ADP . . . Q 9 33.992 14.143 22.251 1 93.12 ? C1' ADP 805 E 1 HETATM 18 N N9 ADP . . . Q 9 33.749 13.929 20.744 1 93.12 ? N9 ADP 805 E 1 HETATM 19 C C8 ADP . . . Q 9 32.691 14.517 20.083 1 93.12 ? C8 ADP 805 E 1 HETATM 20 N N7 ADP . . . Q 9 32.583 14.257 18.791 1 93.12 ? N7 ADP 805 E 1 HETATM 21 C C5 ADP . . . Q 9 33.633 13.435 18.546 1 93.12 ? C5 ADP 805 E 1 HETATM 22 C C6 ADP . . . Q 9 34.127 12.766 17.339 1 93.12 ? C6 ADP 805 E 1 HETATM 23 N N6 ADP . . . Q 9 33.535 12.869 16.124 1 93.12 ? N6 ADP 805 E 1 HETATM 24 N N1 ADP . . . Q 9 35.268 11.973 17.46 1 93.12 ? N1 ADP 805 E 1 HETATM 25 C C2 ADP . . . Q 9 35.908 11.835 18.688 1 93.12 ? C2 ADP 805 E 1 HETATM 26 N N3 ADP . . . Q 9 35.537 12.416 19.878 1 93.12 ? N3 ADP 805 E 1 HETATM 27 C C4 ADP . . . Q 9 34.392 13.213 19.756 1 93.12 ? C4 ADP 805 E 1 # _model_server_stats.io_time_ms 100 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 390 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #