data_6XHI # _model_server_result.job_id rNBODxD6ktv-MxEyC8kWNQ _model_server_result.datetime_utc '2025-08-31 03:54:05' _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 6xhi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 6XHI # _exptl.entry_id 6XHI _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 ? # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? octadecameric 18 'complete point assembly' 1 ? monomeric 1 'point asymmetric unit' 2 ? monomeric 1 'point asymmetric unit, std point frame' 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B 1 (1-18) A,B 2 1 A,B 3 P # 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] P 'transform to point frame' ? ? -0.866028 0.499996 0.00003 0.499996 0.866028 -0.000016 -0.000034 0.000001 -1 78.91249 -294.50672 215.60715 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.766044 0.642788 0.000008 -0.642788 0.766044 0.000022 0.000007 -0.000022 1 -88.14271 189.01992 0.00313 3 'point symmetry operation' ? ? 0.173648 0.984808 0.000029 -0.984808 0.173648 0.000033 0.000027 -0.000034 1 -34.16428 390.47462 0.00145 4 'point symmetry operation' ? ? -0.5 0.866025 0.000052 -0.866025 -0.5 0.000028 0.00005 -0.00003 1 136.67818 510.10121 -0.00425 5 'point symmetry operation' ? ? -0.939693 0.34202 0.000066 -0.34202 -0.939693 0.00001 0.000066 -0.000013 1 344.44559 491.92507 -0.01131 6 'point symmetry operation' ? ? -0.939693 -0.34202 0.000066 0.34202 -0.939693 -0.000013 0.000066 0.00001 1 491.92126 344.45103 -0.01642 7 'point symmetry operation' ? ? -0.5 -0.866025 0.00005 0.866025 -0.5 -0.00003 0.000052 0.000028 1 510.09969 136.68383 -0.01719 8 'point symmetry operation' ? ? 0.173648 -0.984808 0.000027 0.984808 0.173648 -0.000034 0.000029 0.000033 1 390.475 -34.15996 -0.01327 9 'point symmetry operation' ? ? 0.766044 -0.642788 0.000007 0.642788 0.766044 -0.000022 0.000008 0.000022 1 189.02089 -88.14062 -0.00648 10 'point symmetry operation' ? ? 0.500008 -0.866021 -0.000052 -0.866021 -0.500008 0.00003 -0.000052 0.00003 -1 294.51908 510.10159 431.2047 11 'point symmetry operation' ? ? 0.939696 -0.342012 -0.000066 -0.342012 -0.939696 0.000012 -0.000066 0.000012 -1 86.75184 491.92361 431.21173 12 'point symmetry operation' ? ? 0.93969 0.342028 -0.000066 0.342028 -0.93969 -0.000012 -0.000066 -0.000012 -1 -60.72253 344.44826 431.21662 13 'point symmetry operation' ? ? 0.499992 0.86603 -0.00005 0.86603 -0.499992 -0.000029 -0.00005 -0.000029 -1 -78.89912 136.6809 431.21708 14 'point symmetry operation' ? ? -0.173657 0.984806 -0.000027 0.984806 0.173657 -0.000033 -0.000027 -0.000033 -1 40.72709 -34.16183 431.21289 15 'point symmetry operation' ? ? -0.76605 0.642781 -0.000007 0.642781 0.76605 -0.00002 -0.000007 -0.00002 -1 242.18167 -88.1407 431.20602 16 'point symmetry operation' ? ? -1 -0.000009 0 -0.000009 1 0.000001 0 0.000002 -1 431.20178 0.00159 431.19968 17 'point symmetry operation' ? ? -0.766039 -0.642794 -0.000008 -0.642794 0.766039 0.000023 -0.000008 0.000023 -1 519.34282 189.02229 431.19683 18 'point symmetry operation' ? ? -0.173639 -0.984809 -0.000029 -0.984809 0.173639 0.000034 -0.000029 0.000034 -1 465.3626 390.47651 431.19881 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 6XHI _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 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id ADP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 601 _pdbx_nonpoly_scheme.auth_seq_num 556 _pdbx_nonpoly_scheme.pdb_mon_id ADP _pdbx_nonpoly_scheme.auth_mon_id ADP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . B 2 157.026 240.808 189.721 1 101.46 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . B 2 156.748 239.578 188.907 1 101.46 -1 O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . B 2 156.192 241.984 189.316 1 101.46 ? O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . B 2 158.485 241.14 189.822 1 101.46 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . B 2 156.839 241.546 192.354 1 101.46 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . B 2 156.238 242.828 191.9 1 101.46 ? O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . B 2 158.285 241.526 192.709 1 101.46 -1 O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . B 2 156.579 240.485 191.205 1 101.46 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . B 2 155.974 240.954 193.552 1 101.46 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . B 2 154.541 240.975 193.401 1 101.46 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . B 2 153.922 241.028 194.773 1 101.46 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . B 2 154.156 242.353 195.317 1 101.46 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . B 2 152.398 240.89 194.794 1 101.46 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . B 2 151.963 240.665 196.128 1 101.46 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . B 2 152.024 242.319 194.416 1 101.46 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . B 2 150.667 242.622 194.637 1 101.46 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . B 2 152.933 243.048 195.393 1 101.46 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . B 2 153.155 244.444 195.048 1 101.46 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . B 2 153.833 244.924 193.959 1 101.46 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . B 2 153.87 246.231 193.907 1 101.46 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . B 2 153.18 246.639 195.037 1 101.46 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . B 2 152.877 247.912 195.549 1 101.46 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . B 2 153.243 249.046 194.964 1 101.46 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . B 2 152.171 247.971 196.701 1 101.46 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . B 2 151.804 246.824 197.281 1 101.46 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . B 2 152.033 245.574 196.892 1 101.46 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . B 2 152.735 245.547 195.75 1 101.46 ? C4 ADP 601 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 4 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 391 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #