data_1XD9 # _model_server_result.job_id 71VfDs6J4WUEPFzMkvr1VA _model_server_result.datetime_utc '2024-12-15 17:48:53' _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 1xd9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":292}' # _entry.id 1XD9 # _exptl.entry_id 1XD9 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.23 _cell.angle_gamma 90 _cell.entry_id 1XD9 _cell.length_a 57.052 _cell.length_b 92.214 _cell.length_c 61.375 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XD9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 G 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 OG SER 16 A SER 16 1_555 C MG MG . A MG 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc2 A OD1 ASP 43 A ASP 43 1_555 C MG MG . A MG 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.987 ? metalc ? metalc3 A OD2 ASP 43 A ASP 43 1_555 C MG MG . A MG 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc4 A SG CYS 97 A CYS 97 1_555 D FE2 SF4 . A SF4 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc5 A SG CYS 132 A CYS 132 1_555 D FE3 SF4 . A SF4 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc6 D FE1 SF4 . A SF4 290 1_555 B SG CYS 97 B CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc7 D FE4 SF4 . A SF4 290 1_555 B SG CYS 132 B CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc8 B OG SER 16 B SER 16 1_555 F MG MG . B MG 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc9 B OD1 ASP 43 B ASP 43 1_555 F MG MG . B MG 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? metalc ? metalc10 B OD2 ASP 43 B ASP 43 1_555 F MG MG . B MG 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? # _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 1XD9 _atom_sites.fract_transf_matrix[1][1] 0.017528 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00348 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010844 _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] 0.016611 _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 C 2 MG A 1 293 293 MG MG . D 3 SF4 A 1 290 290 SF4 FS4 . E 4 ADP A 1 291 291 ADP ADP . F 2 MG B 1 294 293 MG MG . G 4 ADP B 1 292 292 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 . . . G 4 12.738 -0.789 20.514 1 87.29 ? PB ADP 292 B 1 HETATM 2 O O1B ADP . . . G 4 13.699 -0.888 19.032 1 84.74 ? O1B ADP 292 B 1 HETATM 3 O O2B ADP . . . G 4 13.267 0.455 21.116 1 79.63 ? O2B ADP 292 B 1 HETATM 4 O O3B ADP . . . G 4 11.316 -0.715 20.095 1 85.5 ? O3B ADP 292 B 1 HETATM 5 P PA ADP . . . G 4 13.321 -2.329 22.561 1 87.41 ? PA ADP 292 B 1 HETATM 6 O O1A ADP . . . G 4 14.562 -1.792 23.153 1 80.52 ? O1A ADP 292 B 1 HETATM 7 O O2A ADP . . . G 4 12.077 -2.106 23.369 1 90.34 ? O2A ADP 292 B 1 HETATM 8 O O3A ADP . . . G 4 13.182 -2.092 21.1 1 84.94 ? O3A ADP 292 B 1 HETATM 9 O O5' ADP . . . G 4 13.542 -3.905 22.694 1 83.3 ? O5' ADP 292 B 1 HETATM 10 C C5' ADP . . . G 4 12.637 -4.855 22.122 1 85.36 ? C5' ADP 292 B 1 HETATM 11 C C4' ADP . . . G 4 12.768 -6.336 22.638 1 86.4 ? C4' ADP 292 B 1 HETATM 12 O O4' ADP . . . G 4 14.167 -6.719 22.387 1 85.65 ? O4' ADP 292 B 1 HETATM 13 C C3' ADP . . . G 4 12.55 -6.575 24.205 1 85.67 ? C3' ADP 292 B 1 HETATM 14 O O3' ADP . . . G 4 12.453 -7.972 24.573 1 83.48 ? O3' ADP 292 B 1 HETATM 15 C C2' ADP . . . G 4 13.949 -6.102 24.645 1 85.07 ? C2' ADP 292 B 1 HETATM 16 O O2' ADP . . . G 4 14.13 -6.451 26.027 1 77.42 ? O2' ADP 292 B 1 HETATM 17 C C1' ADP . . . G 4 14.745 -7.023 23.696 1 85.27 ? C1' ADP 292 B 1 HETATM 18 N N9 ADP . . . G 4 16.203 -6.705 23.745 1 84.15 ? N9 ADP 292 B 1 HETATM 19 C C8 ADP . . . G 4 16.853 -5.5 23.626 1 83.73 ? C8 ADP 292 B 1 HETATM 20 N N7 ADP . . . G 4 18.153 -5.575 23.716 1 85.66 ? N7 ADP 292 B 1 HETATM 21 C C5 ADP . . . G 4 18.389 -6.932 23.888 1 85.68 ? C5 ADP 292 B 1 HETATM 22 C C6 ADP . . . G 4 19.569 -7.675 24.039 1 85.45 ? C6 ADP 292 B 1 HETATM 23 N N6 ADP . . . G 4 20.776 -7.132 23.995 1 85.99 ? N6 ADP 292 B 1 HETATM 24 N N1 ADP . . . G 4 19.447 -8.994 24.225 1 89.31 ? N1 ADP 292 B 1 HETATM 25 C C2 ADP . . . G 4 18.229 -9.53 24.233 1 91.29 ? C2 ADP 292 B 1 HETATM 26 N N3 ADP . . . G 4 17.043 -8.956 24.073 1 89.11 ? N3 ADP 292 B 1 HETATM 27 C C4 ADP . . . G 4 17.205 -7.625 23.908 1 86.29 ? C4 ADP 292 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 27 #