data_3THO # _model_server_result.job_id '_tnvLYZi7FwgqGTbIk5FuQ' _model_server_result.datetime_utc '2025-03-04 07:59:19' _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 3tho # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1452}' # _entry.id 3THO # _exptl.entry_id 3THO _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 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 120 _cell.entry_id 3THO _cell.length_a 121.772 _cell.length_b 121.772 _cell.length_c 135.126 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3THO _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 2 1,2 A,C,D,E,F,G,H,I,J,Q 3 1,2 B,K,L,M,N,O,P,R 3 3,4 # 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 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 45.042 3 'crystal symmetry operation' 3_445 -x+y-1,-x-1,z+1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -60.886 -105.457645 45.042 4 'crystal symmetry operation' 4_565 y,x+1,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 -60.886 105.457645 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 disulf ? disulf1 A SG CYS 334 A CYS 804 1_555 A SG CYS 360 A CYS 830 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc1 A OE1 GLU 328 A GLU 798 1_555 D MG MG . A MG 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? metalc ? metalc2 D MG MG . A MG 853 1_555 C O2A ADP . A ADP 1452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.85 ? metalc ? metalc3 K MN MN . B MN 1 1_555 B OD2 ASP 8 B ASP 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc4 K MN MN . B MN 1 1_555 B NE2 HIS 10 B HIS 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? metalc ? metalc5 K MN MN . B MN 1 1_555 B OD2 ASP 52 B ASP 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc6 L MN MN . B MN 2 1_555 B OD2 ASP 52 B ASP 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc7 L MN MN . B MN 2 1_555 B OD1 ASN 87 B ASN 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc8 L MN MN . B MN 2 1_555 B NE2 HIS 174 B HIS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc9 L MN MN . B MN 2 1_555 B ND1 HIS 210 B HIS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? # _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 3THO _atom_sites.fract_transf_matrix[1][1] 0.008212 _atom_sites.fract_transf_matrix[1][2] 0.004741 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009482 _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] 0.0074 _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 3 ADP A 1 1452 1452 ADP ADP . D 4 MG A 1 853 1 MG MG . E 5 SO4 A 1 854 2 SO4 SO4 . F 5 SO4 A 1 855 3 SO4 SO4 . G 5 SO4 A 1 856 6 SO4 SO4 . H 5 SO4 A 1 857 8 SO4 SO4 . I 5 SO4 A 1 858 9 SO4 SO4 . J 6 PO4 A 1 859 1 PO4 PO4 . K 7 MN B 1 1 1 MN MN . L 7 MN B 1 2 2 MN MN . M 5 SO4 B 1 386 1 SO4 SO4 . N 5 SO4 B 1 4 4 SO4 SO4 . O 5 SO4 B 1 5 5 SO4 SO4 . P 5 SO4 B 1 387 7 SO4 SO4 . Q 8 HOH A 1 860 9 HOH HOH . Q 8 HOH A 2 861 11 HOH HOH . Q 8 HOH A 3 862 12 HOH HOH . Q 8 HOH A 4 863 13 HOH HOH . Q 8 HOH A 5 864 15 HOH HOH . Q 8 HOH A 6 865 16 HOH HOH . Q 8 HOH A 7 866 20 HOH HOH . Q 8 HOH A 8 867 21 HOH HOH . Q 8 HOH A 9 868 23 HOH HOH . Q 8 HOH A 10 869 24 HOH HOH . Q 8 HOH A 11 870 30 HOH HOH . Q 8 HOH A 12 871 34 HOH HOH . Q 8 HOH A 13 872 38 HOH HOH . Q 8 HOH A 14 873 39 HOH HOH . Q 8 HOH A 15 874 40 HOH HOH . Q 8 HOH A 16 875 42 HOH HOH . Q 8 HOH A 17 876 43 HOH HOH . Q 8 HOH A 18 877 44 HOH HOH . R 8 HOH B 1 3 3 HOH HOH . R 8 HOH B 2 6 6 HOH HOH . R 8 HOH B 3 388 1 HOH HOH . R 8 HOH B 4 389 2 HOH HOH . R 8 HOH B 5 390 4 HOH HOH . R 8 HOH B 6 391 5 HOH HOH . R 8 HOH B 7 392 7 HOH HOH . R 8 HOH B 8 393 8 HOH HOH . R 8 HOH B 9 394 10 HOH HOH . R 8 HOH B 10 395 14 HOH HOH . R 8 HOH B 11 396 17 HOH HOH . R 8 HOH B 12 397 18 HOH HOH . R 8 HOH B 13 398 19 HOH HOH . R 8 HOH B 14 399 22 HOH HOH . R 8 HOH B 15 400 25 HOH HOH . R 8 HOH B 16 401 26 HOH HOH . R 8 HOH B 17 402 27 HOH HOH . R 8 HOH B 18 403 28 HOH HOH . R 8 HOH B 19 404 29 HOH HOH . R 8 HOH B 20 405 31 HOH HOH . R 8 HOH B 21 406 32 HOH HOH . R 8 HOH B 22 407 33 HOH HOH . R 8 HOH B 23 408 35 HOH HOH . R 8 HOH B 24 409 37 HOH HOH . R 8 HOH B 25 410 41 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 . . . C 3 -42.571 -12.446 24.479 1 42.33 ? PB ADP 1452 A 1 HETATM 2 O O1B ADP . . . C 3 -41.96 -12.179 23.102 1 45.34 ? O1B ADP 1452 A 1 HETATM 3 O O2B ADP . . . C 3 -43.821 -13.36 24.324 1 48.54 ? O2B ADP 1452 A 1 HETATM 4 O O3B ADP . . . C 3 -42.964 -11.144 25.202 1 49.72 ? O3B ADP 1452 A 1 HETATM 5 P PA ADP . . . C 3 -40.172 -13.871 25.145 1 38.97 ? PA ADP 1452 A 1 HETATM 6 O O1A ADP . . . C 3 -40.333 -14.883 24.023 1 41.77 ? O1A ADP 1452 A 1 HETATM 7 O O2A ADP . . . C 3 -39.037 -12.858 24.806 1 42.85 ? O2A ADP 1452 A 1 HETATM 8 O O3A ADP . . . C 3 -41.563 -13.141 25.459 1 46.39 ? O3A ADP 1452 A 1 HETATM 9 O O5' ADP . . . C 3 -39.734 -14.524 26.492 1 46.38 ? O5' ADP 1452 A 1 HETATM 10 C C5' ADP . . . C 3 -40.391 -15.703 26.98 1 45.09 ? C5' ADP 1452 A 1 HETATM 11 C C4' ADP . . . C 3 -40.1 -16.108 28.338 1 49.18 ? C4' ADP 1452 A 1 HETATM 12 O O4' ADP . . . C 3 -38.91 -16.978 28.438 1 46.34 ? O4' ADP 1452 A 1 HETATM 13 C C3' ADP . . . C 3 -39.805 -14.956 29.218 1 45.52 ? C3' ADP 1452 A 1 HETATM 14 O O3' ADP . . . C 3 -40.483 -15.154 30.381 1 46.7 ? O3' ADP 1452 A 1 HETATM 15 C C2' ADP . . . C 3 -38.343 -15.008 29.43 1 42.74 ? C2' ADP 1452 A 1 HETATM 16 O O2' ADP . . . C 3 -37.911 -14.406 30.566 1 43.15 ? O2' ADP 1452 A 1 HETATM 17 C C1' ADP . . . C 3 -38.109 -16.486 29.5 1 41.49 ? C1' ADP 1452 A 1 HETATM 18 N N9 ADP . . . C 3 -36.75 -16.957 29.364 1 43.71 ? N9 ADP 1452 A 1 HETATM 19 C C8 ADP . . . C 3 -35.665 -16.283 28.912 1 44.41 ? C8 ADP 1452 A 1 HETATM 20 N N7 ADP . . . C 3 -34.608 -17.114 28.945 1 38.56 ? N7 ADP 1452 A 1 HETATM 21 C C5 ADP . . . C 3 -35.029 -18.317 29.408 1 46.42 ? C5 ADP 1452 A 1 HETATM 22 C C6 ADP . . . C 3 -34.405 -19.558 29.64 1 43.34 ? C6 ADP 1452 A 1 HETATM 23 N N6 ADP . . . C 3 -33.032 -19.766 29.371 1 41.72 ? N6 ADP 1452 A 1 HETATM 24 N N1 ADP . . . C 3 -35.139 -20.566 30.126 1 45.33 ? N1 ADP 1452 A 1 HETATM 25 C C2 ADP . . . C 3 -36.461 -20.433 30.378 1 44.6 ? C2 ADP 1452 A 1 HETATM 26 N N3 ADP . . . C 3 -37.087 -19.274 30.153 1 48.7 ? N3 ADP 1452 A 1 HETATM 27 C C4 ADP . . . C 3 -36.399 -18.213 29.676 1 44.95 ? C4 ADP 1452 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #