data_3SHF # _model_server_result.job_id fEH8dDvbLFFCReEOGkT6vA _model_server_result.datetime_utc '2025-03-06 01:04:17' _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 3shf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1250}' # _entry.id 3SHF # _exptl.entry_id 3SHF _exptl.method 'X-RAY DIFFRACTION' # _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 ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3SHF _cell.length_a 72.88 _cell.length_b 111.82 _cell.length_c 244.27 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SHF _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 640 A CYS 633 1_555 A SG CYS 670 A CYS 663 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf2 A SG CYS 682 A CYS 675 1_555 A SG CYS 712 A CYS 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf3 A SG CYS 711 A CYS 704 1_555 A SG CYS 756 A CYS 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf4 A SG CYS 768 A CYS 761 1_555 A SG CYS 811 A CYS 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf5 A SG CYS 810 A CYS 803 1_555 A SG CYS 853 A CYS 846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? # _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 3SHF _atom_sites.fract_transf_matrix[1][1] 0.013721 _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] 0.008943 _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] 0.004094 _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 B 2 ADP A 1 1250 900 ADP ADP . C 3 GBL A 1 1251 1 GBL GBL . D 3 GBL A 1 1252 2 GBL GBL . E 4 HOH A 1 1253 1 HOH WAT . E 4 HOH A 2 1254 2 HOH WAT . E 4 HOH A 3 1255 3 HOH WAT . E 4 HOH A 4 1256 4 HOH WAT . E 4 HOH A 5 1257 5 HOH WAT . E 4 HOH A 6 1258 6 HOH WAT . E 4 HOH A 7 1259 7 HOH WAT . E 4 HOH A 8 1260 8 HOH WAT . E 4 HOH A 9 1261 9 HOH WAT . E 4 HOH A 10 1262 10 HOH WAT . E 4 HOH A 11 1263 13 HOH WAT . E 4 HOH A 12 1264 14 HOH WAT . E 4 HOH A 13 1265 15 HOH WAT . E 4 HOH A 14 1266 16 HOH WAT . E 4 HOH A 15 1267 17 HOH WAT . E 4 HOH A 16 1268 18 HOH WAT . E 4 HOH A 17 1269 20 HOH WAT . E 4 HOH A 18 1270 22 HOH WAT . E 4 HOH A 19 1271 24 HOH WAT . E 4 HOH A 20 1272 25 HOH WAT . E 4 HOH A 21 1273 26 HOH WAT . E 4 HOH A 22 1274 32 HOH WAT . E 4 HOH A 23 1275 35 HOH WAT . E 4 HOH A 24 1276 37 HOH WAT . E 4 HOH A 25 1277 40 HOH WAT . E 4 HOH A 26 1278 42 HOH WAT . E 4 HOH A 27 1279 43 HOH WAT . E 4 HOH A 28 1280 45 HOH WAT . E 4 HOH A 29 1281 47 HOH WAT . E 4 HOH A 30 1282 48 HOH WAT . E 4 HOH A 31 1283 51 HOH WAT . E 4 HOH A 32 1284 56 HOH WAT . E 4 HOH A 33 1285 57 HOH WAT . E 4 HOH A 34 1286 58 HOH WAT . E 4 HOH A 35 1287 60 HOH WAT . E 4 HOH A 36 1288 63 HOH WAT . E 4 HOH A 37 1289 66 HOH WAT . E 4 HOH A 38 1290 67 HOH WAT . E 4 HOH A 39 1291 68 HOH WAT . E 4 HOH A 40 1292 69 HOH WAT . E 4 HOH A 41 1293 70 HOH WAT . E 4 HOH A 42 1294 71 HOH WAT . E 4 HOH A 43 1295 73 HOH WAT . E 4 HOH A 44 1296 74 HOH WAT . E 4 HOH A 45 1297 76 HOH WAT . E 4 HOH A 46 1298 77 HOH WAT . E 4 HOH A 47 1299 79 HOH WAT . E 4 HOH A 48 1300 82 HOH WAT . E 4 HOH A 49 1301 83 HOH WAT . E 4 HOH A 50 1302 85 HOH WAT . E 4 HOH A 51 1303 87 HOH WAT . E 4 HOH A 52 1304 88 HOH WAT . E 4 HOH A 53 1305 90 HOH WAT . E 4 HOH A 54 1306 91 HOH WAT . E 4 HOH A 55 1307 92 HOH WAT . E 4 HOH A 56 1308 94 HOH WAT . E 4 HOH A 57 1309 97 HOH WAT . E 4 HOH A 58 1310 98 HOH WAT . E 4 HOH A 59 1311 100 HOH WAT . E 4 HOH A 60 1312 101 HOH WAT . E 4 HOH A 61 1313 102 HOH WAT . E 4 HOH A 62 1314 103 HOH WAT . E 4 HOH A 63 1315 108 HOH WAT . E 4 HOH A 64 1316 111 HOH WAT . E 4 HOH A 65 1317 112 HOH WAT . E 4 HOH A 66 1318 113 HOH WAT . E 4 HOH A 67 1319 114 HOH WAT . E 4 HOH A 68 1320 115 HOH WAT . E 4 HOH A 69 1321 117 HOH WAT . E 4 HOH A 70 1322 118 HOH WAT . E 4 HOH A 71 1323 119 HOH WAT . E 4 HOH A 72 1324 120 HOH WAT . E 4 HOH A 73 1325 121 HOH WAT . # 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 0.065 34.437 -18.087 1 85.14 ? PB ADP 1250 A 1 HETATM 2 O O1B ADP . . . B 2 -0.282 35.453 -19.112 1 83.67 ? O1B ADP 1250 A 1 HETATM 3 O O2B ADP . . . B 2 1.587 34.696 -17.641 1 83.54 ? O2B ADP 1250 A 1 HETATM 4 O O3B ADP . . . B 2 -0.072 32.92 -18.682 1 84.04 ? O3B ADP 1250 A 1 HETATM 5 P PA ADP . . . B 2 -2.514 34.353 -17.133 1 84.25 ? PA ADP 1250 A 1 HETATM 6 O O1A ADP . . . B 2 -3.036 35.289 -18.188 1 81.64 ? O1A ADP 1250 A 1 HETATM 7 O O2A ADP . . . B 2 -2.707 32.799 -17.597 1 82.55 ? O2A ADP 1250 A 1 HETATM 8 O O3A ADP . . . B 2 -0.911 34.637 -16.793 1 84.46 ? O3A ADP 1250 A 1 HETATM 9 O O5' ADP . . . B 2 -3.27 34.602 -15.728 1 83.53 ? O5' ADP 1250 A 1 HETATM 10 C C5' ADP . . . B 2 -4.669 34.388 -15.805 1 84.76 ? C5' ADP 1250 A 1 HETATM 11 C C4' ADP . . . B 2 -5.129 34.671 -14.393 1 85.59 ? C4' ADP 1250 A 1 HETATM 12 O O4' ADP . . . B 2 -4.758 36.031 -13.996 1 85.69 ? O4' ADP 1250 A 1 HETATM 13 C C3' ADP . . . B 2 -6.655 34.509 -14.192 1 87.63 ? C3' ADP 1250 A 1 HETATM 14 O O3' ADP . . . B 2 -6.932 33.513 -13.204 1 87.79 ? O3' ADP 1250 A 1 HETATM 15 C C2' ADP . . . B 2 -7.177 35.942 -13.822 1 88.68 ? C2' ADP 1250 A 1 HETATM 16 O O2' ADP . . . B 2 -7.843 36.041 -12.525 1 87.05 ? O2' ADP 1250 A 1 HETATM 17 C C1' ADP . . . B 2 -5.956 36.868 -13.897 1 88.15 ? C1' ADP 1250 A 1 HETATM 18 N N9 ADP . . . B 2 -6.132 37.766 -15.077 1 89.25 ? N9 ADP 1250 A 1 HETATM 19 C C8 ADP . . . B 2 -5.302 37.89 -16.176 1 89.92 ? C8 ADP 1250 A 1 HETATM 20 N N7 ADP . . . B 2 -5.775 38.784 -17.017 1 90.49 ? N7 ADP 1250 A 1 HETATM 21 C C5 ADP . . . B 2 -6.955 39.303 -16.515 1 90.43 ? C5 ADP 1250 A 1 HETATM 22 C C6 ADP . . . B 2 -7.932 40.298 -16.952 1 90.4 ? C6 ADP 1250 A 1 HETATM 23 N N6 ADP . . . B 2 -7.772 40.985 -18.173 1 88.83 ? N6 ADP 1250 A 1 HETATM 24 N N1 ADP . . . B 2 -9.017 40.545 -16.143 1 88.16 ? N1 ADP 1250 A 1 HETATM 25 C C2 ADP . . . B 2 -9.193 39.9 -14.976 1 86.76 ? C2 ADP 1250 A 1 HETATM 26 N N3 ADP . . . B 2 -8.318 38.981 -14.54 1 87.81 ? N3 ADP 1250 A 1 HETATM 27 C C4 ADP . . . B 2 -7.198 38.652 -15.262 1 89.5 ? C4 ADP 1250 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 118 _model_server_stats.create_model_time_ms 126 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #