data_3R9J # _model_server_result.job_id T3Ok2tGDl3MkinldeMvB9g _model_server_result.datetime_utc '2025-03-05 21:08:16' _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 3r9j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":261}' # _entry.id 3R9J # _exptl.entry_id 3R9J _exptl.method 'X-RAY DIFFRACTION' # _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 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 3R9J _cell.length_a 94.393 _cell.length_b 94.393 _cell.length_c 284.979 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3R9J _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F 1 1 A,B,C,D,E,F 1 2 D 2 3 A,B,C,E,F 2 2 A,B,E,F 3 2 C,D 4 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'crystal symmetry operation' 3_544 -y+1/2,x-1/2,z-1/4 0 -1 0 1 0 0 0 0 1 47.1965 -47.1965 -71.24475 2 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z+1/4 0 1 0 -1 0 0 0 0 1 47.1965 47.1965 71.24475 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N # _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 3R9J _atom_sites.fract_transf_matrix[1][1] 0.010594 _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] 0.010594 _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] 0.003509 _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 E 3 ADP A 1 261 1 ADP ADP . F 3 ADP B 1 261 2 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 . . . E 3 21.55 7.422 39.955 1 135 ? PB ADP 261 A 1 HETATM 2 O O1B ADP . . . E 3 21.038 6.338 39.061 1 135 ? O1B ADP 261 A 1 HETATM 3 O O2B ADP . . . E 3 21.714 6.939 41.37 1 135 ? O2B ADP 261 A 1 HETATM 4 O O3B ADP . . . E 3 22.837 8.04 39.394 1 135 ? O3B ADP 261 A 1 HETATM 5 P PA ADP . . . E 3 19.641 9.057 41.18 1 135 ? PA ADP 261 A 1 HETATM 6 O O1A ADP . . . E 3 20.642 9.89 41.944 1 135 ? O1A ADP 261 A 1 HETATM 7 O O2A ADP . . . E 3 18.882 8.025 42.034 1 135 ? O2A ADP 261 A 1 HETATM 8 O O3A ADP . . . E 3 20.416 8.468 39.955 1 135 ? O3A ADP 261 A 1 HETATM 9 O O5' ADP . . . E 3 18.563 10.013 40.507 1 135 ? O5' ADP 261 A 1 HETATM 10 C C5' ADP . . . E 3 18.897 10.834 39.364 1 135 ? C5' ADP 261 A 1 HETATM 11 C C4' ADP . . . E 3 17.943 12.043 39.367 1 135 ? C4' ADP 261 A 1 HETATM 12 O O4' ADP . . . E 3 16.597 11.739 38.979 1 135 ? O4' ADP 261 A 1 HETATM 13 C C3' ADP . . . E 3 17.82 12.717 40.706 1 135 ? C3' ADP 261 A 1 HETATM 14 O O3' ADP . . . E 3 17.924 14.114 40.459 1 135 ? O3' ADP 261 A 1 HETATM 15 C C2' ADP . . . E 3 16.465 12.28 41.26 1 135 ? C2' ADP 261 A 1 HETATM 16 O O2' ADP . . . E 3 15.907 13.327 42.07 1 135 ? O2' ADP 261 A 1 HETATM 17 C C1' ADP . . . E 3 15.645 12.161 39.997 1 135 ? C1' ADP 261 A 1 HETATM 18 N N9 ADP . . . E 3 14.62 11.121 40.058 1 135 ? N9 ADP 261 A 1 HETATM 19 C C8 ADP . . . E 3 14.837 9.767 40.236 1 135 ? C8 ADP 261 A 1 HETATM 20 N N7 ADP . . . E 3 13.696 9.074 40.225 1 135 ? N7 ADP 261 A 1 HETATM 21 C C5 ADP . . . E 3 12.694 10.005 40.043 1 135 ? C5 ADP 261 A 1 HETATM 22 C C6 ADP . . . E 3 11.266 9.908 39.948 1 135 ? C6 ADP 261 A 1 HETATM 23 N N6 ADP . . . E 3 10.59 8.731 40.044 1 135 ? N6 ADP 261 A 1 HETATM 24 N N1 ADP . . . E 3 10.54 11.035 39.765 1 135 ? N1 ADP 261 A 1 HETATM 25 C C2 ADP . . . E 3 11.193 12.221 39.676 1 135 ? C2 ADP 261 A 1 HETATM 26 N N3 ADP . . . E 3 12.544 12.435 39.745 1 135 ? N3 ADP 261 A 1 HETATM 27 C C4 ADP . . . E 3 13.254 11.293 39.935 1 135 ? C4 ADP 261 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 214 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #