0.009522 0.000000 0.000000 0.000000 0.009522 0.000000 0.000000 0.000000 0.009522 0.00000 0.00000 0.00000 Komander, D. Odenwaelder, P. Barford, D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 48 90.00 90.00 90.00 105.021 105.021 105.021 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking Cd 2 112.411 CADMIUM ION non-polymer Cl -1 35.453 CHLORIDE ION non-polymer Co 2 58.933 COBALT (II) ION non-polymer C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking Mg 2 24.305 MAGNESIUM ION non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N CD N 75 N CL N 76 N CO N 77 N N N 78 S C N 79 N C N 80 N O N 81 N C N 82 N C N 83 N C N 84 N O N 85 N N N 86 N O N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N N N 98 S C N 99 N C N 100 N O N 101 N C N 102 N C N 103 N C N 104 N O N 105 N O N 106 N O N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N N N 117 N C N 118 N C N 119 N O N 120 N O N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N N N 127 S C N 128 N C N 129 N O N 130 N C Y 131 N C Y 132 N N Y 133 N C Y 134 N C Y 135 N N N 136 N O N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N O N 148 N H N 149 N H N 150 N N N 151 S C N 152 N C N 153 N O N 154 S C N 155 N C N 156 N C N 157 N C N 158 N O N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N N N 173 S C N 174 N C N 175 N O N 176 N C N 177 N C N 178 N C N 179 N C N 180 N O N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N N N 195 S C N 196 N C N 197 N O N 198 N C N 199 N C N 200 N C N 201 N C N 202 N N N 203 N O N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N N N 220 S C N 221 N C N 222 N O N 223 N C N 224 N C N 225 N S N 226 N C N 227 N O N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N MG N 240 N N N 241 S C N 242 N C N 243 N O N 244 N C Y 245 N C Y 246 N C Y 247 N C Y 248 N C Y 249 N C Y 250 N C N 251 N O N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N N N 264 S C N 265 N C N 266 N O N 267 N C N 268 N C N 269 N C N 270 N O N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N N N 281 S C N 282 N C N 283 N O N 284 N C N 285 N O N 286 N O N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N N N 295 S C N 296 N C N 297 N O N 298 R C N 299 N O N 300 N C N 301 N O N 302 N H N 303 N H N 304 N H N 305 N H N 306 N H N 307 N H N 308 N H N 309 N H N 310 N H N 311 N N N 312 S C N 313 N C N 314 N O N 315 N C Y 316 N C Y 317 N C Y 318 N C Y 319 N C Y 320 N C Y 321 N C N 322 N O N 323 N O N 324 N H N 325 N H N 326 N H N 327 N H N 328 N H N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N N N 336 S C N 337 N C N 338 N O N 339 N C N 340 N C N 341 N C N 342 N O N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N H N 352 N H N 353 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N doub N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N doub N 123 N sing N 124 N sing N 125 N sing N 126 N sing Y 127 N sing Y 128 N doub Y 129 N doub N 130 N sing Y 131 N sing N 132 N sing Y 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N doub N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N doub N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N doub N 231 N sing N 232 N sing N 233 N sing N 234 N sing Y 235 N doub Y 236 N sing Y 237 N sing N 238 N sing Y 239 N doub N 240 N sing Y 241 N doub N 242 N sing Y 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N doub N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N doub N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N doub N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N doub N 300 N sing N 301 N sing N 302 N sing N 303 N sing Y 304 N doub Y 305 N sing Y 306 N sing N 307 N sing Y 308 N doub N 309 N sing Y 310 N doub N 311 N sing Y 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N doub N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing UK Embo Rep. 1469-221X 10 466 10.1038/EMBOR.2009.55 19373254 Molecular Discrimination of Structurally Equivalent Lys 63-Linked and Linear Polyubiquitin Chains. 2009 10.2210/pdb2jf5/pdb pdb_00002jf5 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2006-10-09 ADSC CCD SINGLE WAVELENGTH M x-ray 1 0.8726 1.0 ID23-2 ESRF 0.8726 SYNCHROTRON ESRF BEAMLINE ID23-2 ISO-PEPTIDE LINK BETWEEN A-LYS63 AND B-GLY76 8576.831 UBIQUITIN 2 man polymer 112.411 CADMIUM ION 2 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 58.933 COBALT (II) ION 2 syn non-polymer 35.453 CHLORIDE ION 1 syn non-polymer 18.015 water 78 nat water DI-UBIQUITIN, LYS63-LINKED no no MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG A,B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n HUMAN sample 9606 HOMO SAPIENS 562 ESCHERICHIA COLI ROSETTA2 PLYSS PET17B 1 2.83 56 NONE 7.5 12 % (W/V) PEG 3350, 5 MM NICKEL CHLORIDE, 5 MM COBALT CHLORIDE, 5 MM CADMIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 0.1 M HEPES [PH 7.5] chem_comp_atom chem_comp_bond database_2 pdbx_database_status pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_site repository Initial release Advisory Refinement description Version format compliance Data collection Database references Derived calculations Other Refinement description 1 0 2008-02-05 1 1 2011-07-13 1 2 2023-12-13 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_sf _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_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_symmetry _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _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_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURALSPECIFICITY UBIQUITIN NMR STRUCTURE STRUCTURE OF A NEW CRYSTAL FORM OF TETRAUBIQUITIN STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTERCOMPLEX STRUCTURE OF RECOMBINANT HUMAN UBIQUITIN IN AOT REVERSEMICELLES SOLUTION STRUCTURE OF A DIMERIC N-TERMINAL FRAGMENT OF HUMAN UBIQUITIN CRYSTAL STRUCTURE OF A UBP-FAMILY DEUBIQUITINATING ENZYMEIN ISOLATION AND IN COMPLEX WITH UBIQUITIN ALDEHYDE SYNTHETIC UBIQUITIN WITH FLUORO-LEU AT 50 AND 67 UBIQUITIN RECOGNITION BY NPL4 ZINC-FINGERS TSG101(UEV) DOMAIN IN COMPLEX WITH UBIQUITIN CRYSTAL STRUCTURE OF A MULTIPLE HYDROPHOBIC CORE MUTANT OFUBIQUITIN TETRAUBIQUITIN UBIQUITIN UBIQUITIN CRYSTAL STRUCTURE OF UCHL3-UBVME COMPLEX SIMULTANEOUS DETERMINATION OF PROTEIN STRUCTURE AND DYNAMICS SOLUTION STRUCTURE OF S5A UIM-1/UBIQUITIN COMPLEX SOLUTION STRUCTURE OF S5A UIM-2/UBIQUITIN COMPLEX SOLUTION STRUCTURE OF THE HUMAN MMS2- UBIQUITIN COMPLEX STRUCTURE OF USP14 BOUND TO UBQUITIN ALDEHYDE NMR STRUCTURE OF LYS48-LINKED DI-UBIQUITIN USING CHEMICAL SHIFT PERTURBATION DATA TOGETHER WITH RDCS AND 15N-RELAXATION DATA X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED [D-GLN35]UBIQUITIN WITH A CUBIC SPACE GROUP X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED [D-VAL35]UBIQUITIN WITH A CUBIC SPACE GROUP X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZEDUBIQUITIN WITH A CUBIC SPACE GROUP X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED [L-GLN35]UBIQUITIN WITH A CUBIC SPACE GROUP SOLUTION STRUCTURE OF THE UBCH5C/UB NON- COVALENT COMPLEX CO-CRYSTAL STRUCTURE OF ZNF UBP DOMAIN FROM THEDEUBIQUITINATING ENZYME ISOPEPTIDASE T (ISOT) IN COMPLEXWITH UBIQUITIN CRYSTAL STRUCTURE OF THE 9-10 MOAD INSERTION MUTANT OFUBIQUITIN CRYSTAL STRUCTURE OF THE 35-36 8 GLYCINE INSERTION MUTANTOF UBIQUITIN CRYSTAL STRUCTURE OF THE 35-36 8 GLYCINE INSERTION MUTANTOF UBIQUITIN CRYSTAL STRUCTURE OF THE UBIQUITIN-SPECIFIC PROTEASE ENCODED BY MURINE CYTOMEGALOVIRUS TEGUMENT PROTEIN M48 IN COMPLEX WITH A UBQUITIN-BASED SUICIDE SUBSTRATE PDBE Y PDBE 2007-01-26 REL REL CD CADMIUM ION MG MAGNESIUM ION CO COBALT (II) ION CL CHLORIDE ION HOH water 1UBQ PDB ENTRY 1UBQ PDB experimental model CD 1076 2 CD CD 1076 A MG 1078 3 MG MG 1078 A CD 1077 2 CD CD 1077 B CO 1079 4 CO CO 1079 B CL 1080 5 CL CL 1080 B CO 1081 4 CO CO 1081 B HOH 2001 6 HOH HOH 2001 A HOH 2002 6 HOH HOH 2002 A HOH 2003 6 HOH HOH 2003 A HOH 2004 6 HOH HOH 2004 A HOH 2005 6 HOH HOH 2005 A HOH 2006 6 HOH HOH 2006 A HOH 2007 6 HOH HOH 2007 A HOH 2008 6 HOH HOH 2008 A HOH 2009 6 HOH HOH 2009 A HOH 2010 6 HOH HOH 2010 A HOH 2011 6 HOH HOH 2011 A HOH 2012 6 HOH HOH 2012 A HOH 2013 6 HOH HOH 2013 A HOH 2014 6 HOH HOH 2014 A HOH 2015 6 HOH HOH 2015 A HOH 2016 6 HOH HOH 2016 A HOH 2017 6 HOH HOH 2017 A HOH 2018 6 HOH HOH 2018 A HOH 2019 6 HOH HOH 2019 A HOH 2020 6 HOH HOH 2020 A HOH 2021 6 HOH HOH 2021 A HOH 2022 6 HOH HOH 2022 A HOH 2023 6 HOH HOH 2023 A HOH 2024 6 HOH HOH 2024 A HOH 2025 6 HOH HOH 2025 A HOH 2026 6 HOH HOH 2026 A HOH 2027 6 HOH HOH 2027 A HOH 2028 6 HOH HOH 2028 A HOH 2029 6 HOH HOH 2029 A HOH 2030 6 HOH HOH 2030 A HOH 2031 6 HOH HOH 2031 A HOH 2001 6 HOH HOH 2001 B HOH 2002 6 HOH HOH 2002 B HOH 2003 6 HOH HOH 2003 B HOH 2004 6 HOH HOH 2004 B HOH 2005 6 HOH HOH 2005 B HOH 2006 6 HOH HOH 2006 B HOH 2007 6 HOH HOH 2007 B HOH 2008 6 HOH HOH 2008 B HOH 2009 6 HOH HOH 2009 B HOH 2010 6 HOH HOH 2010 B HOH 2011 6 HOH HOH 2011 B HOH 2012 6 HOH HOH 2012 B HOH 2013 6 HOH HOH 2013 B HOH 2014 6 HOH HOH 2014 B HOH 2015 6 HOH HOH 2015 B HOH 2016 6 HOH HOH 2016 B HOH 2017 6 HOH HOH 2017 B HOH 2018 6 HOH HOH 2018 B HOH 2019 6 HOH HOH 2019 B HOH 2020 6 HOH HOH 2020 B HOH 2021 6 HOH HOH 2021 B HOH 2022 6 HOH HOH 2022 B HOH 2023 6 HOH HOH 2023 B HOH 2024 6 HOH HOH 2024 B HOH 2025 6 HOH HOH 2025 B HOH 2026 6 HOH HOH 2026 B HOH 2027 6 HOH HOH 2027 B HOH 2028 6 HOH HOH 2028 B HOH 2029 6 HOH HOH 2029 B HOH 2030 6 HOH HOH 2030 B HOH 2031 6 HOH HOH 2031 B HOH 2032 6 HOH HOH 2032 B HOH 2033 6 HOH HOH 2033 B HOH 2034 6 HOH HOH 2034 B HOH 2035 6 HOH HOH 2035 B HOH 2036 6 HOH HOH 2036 B HOH 2037 6 HOH HOH 2037 B HOH 2038 6 HOH HOH 2038 B HOH 2039 6 HOH HOH 2039 B HOH 2040 6 HOH HOH 2040 B HOH 2041 6 HOH HOH 2041 B HOH 2042 6 HOH HOH 2042 B HOH 2043 6 HOH HOH 2043 B HOH 2044 6 HOH HOH 2044 B HOH 2045 6 HOH HOH 2045 B HOH 2046 6 HOH HOH 2046 B HOH 2047 6 HOH HOH 2047 B MET 1 n 1 MET 1 A GLN 2 n 2 GLN 2 A ILE 3 n 3 ILE 3 A PHE 4 n 4 PHE 4 A VAL 5 n 5 VAL 5 A LYS 6 n 6 LYS 6 A THR 7 n 7 THR 7 A LEU 8 n 8 LEU 8 A THR 9 n 9 THR 9 A GLY 10 n 10 GLY 10 A LYS 11 n 11 LYS 11 A THR 12 n 12 THR 12 A ILE 13 n 13 ILE 13 A THR 14 n 14 THR 14 A LEU 15 n 15 LEU 15 A GLU 16 n 16 GLU 16 A VAL 17 n 17 VAL 17 A GLU 18 n 18 GLU 18 A PRO 19 n 19 PRO 19 A SER 20 n 20 SER 20 A ASP 21 n 21 ASP 21 A THR 22 n 22 THR 22 A ILE 23 n 23 ILE 23 A GLU 24 n 24 GLU 24 A ASN 25 n 25 ASN 25 A VAL 26 n 26 VAL 26 A LYS 27 n 27 LYS 27 A ALA 28 n 28 ALA 28 A LYS 29 n 29 LYS 29 A ILE 30 n 30 ILE 30 A GLN 31 n 31 GLN 31 A ASP 32 n 32 ASP 32 A LYS 33 n 33 LYS 33 A GLU 34 n 34 GLU 34 A GLY 35 n 35 GLY 35 A ILE 36 n 36 ILE 36 A PRO 37 n 37 PRO 37 A PRO 38 n 38 PRO 38 A ASP 39 n 39 ASP 39 A GLN 40 n 40 GLN 40 A GLN 41 n 41 GLN 41 A ARG 42 n 42 ARG 42 A LEU 43 n 43 LEU 43 A ILE 44 n 44 ILE 44 A PHE 45 n 45 PHE 45 A ALA 46 n 46 ALA 46 A GLY 47 n 47 GLY 47 A LYS 48 n 48 LYS 48 A GLN 49 n 49 GLN 49 A LEU 50 n 50 LEU 50 A GLU 51 n 51 GLU 51 A ASP 52 n 52 ASP 52 A GLY 53 n 53 GLY 53 A ARG 54 n 54 ARG 54 A THR 55 n 55 THR 55 A LEU 56 n 56 LEU 56 A SER 57 n 57 SER 57 A ASP 58 n 58 ASP 58 A TYR 59 n 59 TYR 59 A ASN 60 n 60 ASN 60 A ILE 61 n 61 ILE 61 A GLN 62 n 62 GLN 62 A LYS 63 n 63 LYS 63 A GLU 64 n 64 GLU 64 A SER 65 n 65 SER 65 A THR 66 n 66 THR 66 A LEU 67 n 67 LEU 67 A HIS 68 n 68 HIS 68 A LEU 69 n 69 LEU 69 A VAL 70 n 70 VAL 70 A LEU 71 n 71 LEU 71 A ARG 72 n 72 ARG 72 A LEU 73 n 73 LEU 73 A ARG 74 n 74 ARG 74 A GLY 75 n 75 GLY 75 A n 76 76 A MET 1 n 1 MET 1 B GLN 2 n 2 GLN 2 B ILE 3 n 3 ILE 3 B PHE 4 n 4 PHE 4 B VAL 5 n 5 VAL 5 B LYS 6 n 6 LYS 6 B THR 7 n 7 THR 7 B LEU 8 n 8 LEU 8 B THR 9 n 9 THR 9 B GLY 10 n 10 GLY 10 B LYS 11 n 11 LYS 11 B THR 12 n 12 THR 12 B ILE 13 n 13 ILE 13 B THR 14 n 14 THR 14 B LEU 15 n 15 LEU 15 B GLU 16 n 16 GLU 16 B VAL 17 n 17 VAL 17 B GLU 18 n 18 GLU 18 B PRO 19 n 19 PRO 19 B SER 20 n 20 SER 20 B ASP 21 n 21 ASP 21 B THR 22 n 22 THR 22 B ILE 23 n 23 ILE 23 B GLU 24 n 24 GLU 24 B ASN 25 n 25 ASN 25 B VAL 26 n 26 VAL 26 B LYS 27 n 27 LYS 27 B ALA 28 n 28 ALA 28 B LYS 29 n 29 LYS 29 B ILE 30 n 30 ILE 30 B GLN 31 n 31 GLN 31 B ASP 32 n 32 ASP 32 B LYS 33 n 33 LYS 33 B GLU 34 n 34 GLU 34 B GLY 35 n 35 GLY 35 B ILE 36 n 36 ILE 36 B PRO 37 n 37 PRO 37 B PRO 38 n 38 PRO 38 B ASP 39 n 39 ASP 39 B GLN 40 n 40 GLN 40 B GLN 41 n 41 GLN 41 B ARG 42 n 42 ARG 42 B LEU 43 n 43 LEU 43 B ILE 44 n 44 ILE 44 B PHE 45 n 45 PHE 45 B ALA 46 n 46 ALA 46 B GLY 47 n 47 GLY 47 B LYS 48 n 48 LYS 48 B GLN 49 n 49 GLN 49 B LEU 50 n 50 LEU 50 B GLU 51 n 51 GLU 51 B ASP 52 n 52 ASP 52 B GLY 53 n 53 GLY 53 B ARG 54 n 54 ARG 54 B THR 55 n 55 THR 55 B LEU 56 n 56 LEU 56 B SER 57 n 57 SER 57 B ASP 58 n 58 ASP 58 B TYR 59 n 59 TYR 59 B ASN 60 n 60 ASN 60 B ILE 61 n 61 ILE 61 B GLN 62 n 62 GLN 62 B LYS 63 n 63 LYS 63 B GLU 64 n 64 GLU 64 B SER 65 n 65 SER 65 B THR 66 n 66 THR 66 B LEU 67 n 67 LEU 67 B HIS 68 n 68 HIS 68 B LEU 69 n 69 LEU 69 B VAL 70 n 70 VAL 70 B LEU 71 n 71 LEU 71 B ARG 72 n 72 ARG 72 B LEU 73 n 73 LEU 73 B ARG 74 n 74 ARG 74 B GLY 75 n 75 GLY 75 B GLY 76 n 76 GLY 76 B 6.1560 2.4955 2.2819 8.1923 0.4569 2.6521 0.1544 -0.0981 -0.6355 -0.3481 0.1542 -0.5479 0.1225 -0.0570 -0.3087 -0.2522 -0.0928 0.0305 -0.2524 -0.0305 -0.1952 refined 63.7127 81.3647 32.5458 X-RAY DIFFRACTION 6.8428 -0.0214 0.8271 4.4467 -0.3700 4.2658 -0.0068 -0.1890 -0.1400 -0.3220 0.1050 0.3767 0.1703 -0.3784 -0.0982 -0.2492 -0.0389 -0.0918 -0.2303 0.0329 -0.2334 refined 92.3340 105.8642 43.9216 X-RAY DIFFRACTION A 1 A 75 X-RAY DIFFRACTION 1 B 1 B 76 X-RAY DIFFRACTION 2 software_defined_assembly PQS 2 dimeric 220 0.6 10810 A MET 1 A N MET 1 1_555 A MG 1078 D MG MG 1_555 A GLU 16 A OE2 GLU 16 1_555 93.5 A MET 1 A N MET 1 1_555 A MG 1078 D MG MG 1_555 A HOH 2005 I O HOH 1_555 121.1 A GLU 16 A OE2 GLU 16 1_555 A MG 1078 D MG MG 1_555 A HOH 2005 I O HOH 1_555 100.2 A GLU 18 A OE2 GLU 18 1_555 A CD 1076 A C CD CD 1_555 A GLU 18 A OE2 GLU 18 12_664 117.8 A GLU 18 A OE2 GLU 18 1_555 A CD 1076 A C CD CD 1_555 A ASP 21 A OD1 ASP 21 1_555 130.1 A GLU 18 A OE2 GLU 18 12_664 A CD 1076 A C CD CD 1_555 A ASP 21 A OD1 ASP 21 1_555 101.4 A GLU 18 A OE1 GLU 18 12_664 A CD 1076 B C CD CD 1_555 A ASP 21 A OD1 ASP 21 1_555 83.1 A GLU 18 A OE1 GLU 18 12_664 A CD 1076 B C CD CD 1_555 A ASP 21 A OD2 ASP 21 1_555 130.7 A ASP 21 A OD1 ASP 21 1_555 A CD 1076 B C CD CD 1_555 A ASP 21 A OD2 ASP 21 1_555 53.6 B MET 1 B N MET 1 1_555 B CO 1079 F CO CO 1_555 B GLU 16 B OE2 GLU 16 1_555 90.5 B MET 1 B N MET 1 1_555 B CO 1079 F CO CO 1_555 B ASP 32 B OD2 ASP 32 7_674 90.8 B GLU 16 B OE2 GLU 16 1_555 B CO 1079 F CO CO 1_555 B ASP 32 B OD2 ASP 32 7_674 93.2 B MET 1 B N MET 1 1_555 B CO 1079 F CO CO 1_555 B HOH 2047 J O HOH 1_555 110.6 B GLU 16 B OE2 GLU 16 1_555 B CO 1079 F CO CO 1_555 B HOH 2047 J O HOH 1_555 140.7 B ASP 32 B OD2 ASP 32 7_674 B CO 1079 F CO CO 1_555 B HOH 2047 J O HOH 1_555 118.1 B GLU 18 B OE1 GLU 18 1_555 B CD 1077 B E CD CD 1_555 B GLU 18 B OE1 GLU 18 10_756 124.9 B GLU 18 B OE1 GLU 18 1_555 B CD 1077 B E CD CD 1_555 B ASP 21 B OD1 ASP 21 1_555 121.4 B GLU 18 B OE1 GLU 18 10_756 B CD 1077 B E CD CD 1_555 B ASP 21 B OD1 ASP 21 1_555 102.1 B GLU 18 B OE2 GLU 18 10_756 B CD 1077 A E CD CD 1_555 B GLU 18 B OE1 GLU 18 10_756 49.5 B GLU 18 B OE2 GLU 18 10_756 B CD 1077 A E CD CD 1_555 B ASP 21 B OD1 ASP 21 1_555 95.5 B GLU 18 B OE1 GLU 18 10_756 B CD 1077 A E CD CD 1_555 B ASP 21 B OD1 ASP 21 1_555 93.9 B GLU 18 B OE2 GLU 18 10_756 B CD 1077 A E CD CD 1_555 B ASP 21 B OD2 ASP 21 1_555 126.8 B GLU 18 B OE1 GLU 18 10_756 B CD 1077 A E CD CD 1_555 B ASP 21 B OD2 ASP 21 1_555 146.4 B ASP 21 B OD1 ASP 21 1_555 B CD 1077 A E CD CD 1_555 B ASP 21 B OD2 ASP 21 1_555 52.6 B GLU 18 B OE2 GLU 18 10_756 B CD 1077 A E CD CD 1_555 B LYS 29 B NZ LYS 29 1_555 75.3 B GLU 18 B OE1 GLU 18 10_756 B CD 1077 A E CD CD 1_555 B LYS 29 B NZ LYS 29 1_555 114.9 B ASP 21 B OD1 ASP 21 1_555 B CD 1077 A E CD CD 1_555 B LYS 29 B NZ LYS 29 1_555 126.9 B ASP 21 B OD2 ASP 21 1_555 B CD 1077 A E CD CD 1_555 B LYS 29 B NZ LYS 29 1_555 91.3 B GLU 18 B OE2 GLU 18 10_756 B CD 1077 A E CD CD 1_555 B CL 1080 G CL CL 1_555 126.6 B GLU 18 B OE1 GLU 18 10_756 B CD 1077 A E CD CD 1_555 B CL 1080 G CL CL 1_555 110.9 B ASP 21 B OD1 ASP 21 1_555 B CD 1077 A E CD CD 1_555 B CL 1080 G CL CL 1_555 137.8 B ASP 21 B OD2 ASP 21 1_555 B CD 1077 A E CD CD 1_555 B CL 1080 G CL CL 1_555 96.1 B LYS 29 B NZ LYS 29 1_555 B CD 1077 A E CD CD 1_555 B CL 1080 G CL CL 1_555 73.4 B GLU 64 B OE1 GLU 64 1_555 B CO 1081 H CO CO 1_555 B HIS 68 B NE2 HIS 68 24_676 97.7 B GLU 64 B OE1 GLU 64 1_555 B CO 1081 H CO CO 1_555 B HOH 2039 J O HOH 1_555 68.3 B HIS 68 B NE2 HIS 68 24_676 B CO 1081 H CO CO 1_555 B HOH 2039 J O HOH 1_555 63.6 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N LEU 15 A N LEU 15 A O ILE 3 A O ILE 3 A N LYS 6 A N LYS 6 A O LEU 67 A O LEU 67 A N VAL 70 A N VAL 70 A O ARG 42 A O ARG 42 A N PHE 45 A N PHE 45 A O LYS 48 A O LYS 48 B N LEU 15 B N LEU 15 B O ILE 3 B O ILE 3 B N LYS 6 B N LYS 6 B O LEU 67 B O LEU 67 B N VAL 70 B N VAL 70 B O ARG 42 B O ARG 42 B N PHE 45 B N PHE 45 B O LYS 48 B O LYS 48 1 A HOH 2006 I HOH 1 A GLY 76 A GLY 76 1 Y 1 A B NZ C LYS GLY 63 76 1.29 1 B B OE2 O GLU HOH 64 2039 1.92 1 B B O O HOH HOH 2008 2028 2.13 1 B B C O GLY GLY 76 76 0.159 0.016 1.232 1.391 N 42.28 0.944 0.919 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.DISORDERED RESIDUES HAVE BEEN REFINED WITH OCCU 0.01. GLY76 IN MOLA IS NOT MODELLED AN ISOPEPTIDE LINKAGE BETWEEN LYS63 (MOLA) AND GLY76 CONNECTS THE TWO UBIQUITIN MOIETIES 0.250 0.206 0.208 1.95 50.00 756 14211 5.100 99.8 7.283 0.119 RANDOM LIKELY RESIDUAL 1 THROUGHOUT MOLECULAR REPLACEMENT 0.157 0.151 0.80 0.80 1.40 PDB ENTRY 1UBQ MAXIMUM LIKELIHOOD MASK 1.95 50.00 78 1282 6 0 1198 0.016 0.022 1240 1.513 1.998 1671 6.116 5.000 157 36.390 25.439 57 17.114 15.000 258 19.802 15.000 9 0.105 0.200 198 0.006 0.020 897 0.216 0.200 471 0.309 0.200 807 0.232 0.200 76 0.207 0.200 69 0.191 0.200 15 0.887 1.500 789 1.432 2.000 1243 2.226 3.000 492 3.713 4.500 424 0.3320 0.2770 2.00 45 1014 20 1.95 50.00 2JF5 15023 2.0 0.11 1 11.40 5.8 99.9 0.59 1.95 2.06 2.20 1 5.3 100.0 refinement REFMAC 5.2.0019 data reduction MOSFLM data scaling SCALA phasing PHASER crystal structure of Lys63-linked di-ubiquitin 1 N N 1 N N 2 N N 3 N N 2 N N 4 N N 5 N N 4 N N 6 N N 6 N N A THR 22 A THR 22 HELX_P A GLY 35 A GLY 35 1 1 14 A PRO 37 A PRO 37 HELX_P A ASP 39 A ASP 39 5 2 3 A LEU 56 A LEU 56 HELX_P A ASN 60 A ASN 60 5 3 5 B THR 22 B THR 22 HELX_P B GLY 35 B GLY 35 1 4 14 B PRO 37 B PRO 37 HELX_P B ASP 39 B ASP 39 5 5 3 B LEU 56 B LEU 56 HELX_P B ASN 60 B ASN 60 5 6 5 metalc 1.706 A MET 1 A N MET 1 1_555 A MG 1078 D MG MG 1_555 metalc 2.069 A GLU 16 A OE2 GLU 16 1_555 A MG 1078 D MG MG 1_555 metalc 2.101 A A GLU 18 A OE2 GLU 18 1_555 A CD 1076 C CD CD 1_555 metalc 2.597 A A GLU 18 A OE2 GLU 18 12_664 A CD 1076 C CD CD 1_555 metalc 2.400 B A GLU 18 A OE1 GLU 18 12_664 A CD 1076 C CD CD 1_555 metalc 2.165 A A ASP 21 A OD1 ASP 21 1_555 A CD 1076 C CD CD 1_555 metalc 2.174 B A ASP 21 A OD1 ASP 21 1_555 A CD 1076 C CD CD 1_555 metalc 2.640 B A ASP 21 A OD2 ASP 21 1_555 A CD 1076 C CD CD 1_555 metalc 1.881 A MG 1078 D MG MG 1_555 A HOH 2005 I O HOH 1_555 metalc 1.864 B MET 1 B N MET 1 1_555 B CO 1079 F CO CO 1_555 metalc 2.364 B GLU 16 B OE2 GLU 16 1_555 B CO 1079 F CO CO 1_555 metalc 2.344 B B GLU 18 B OE1 GLU 18 1_555 B CD 1077 E CD CD 1_555 metalc 2.502 B B GLU 18 B OE1 GLU 18 10_756 B CD 1077 E CD CD 1_555 metalc 2.234 A B GLU 18 B OE2 GLU 18 10_756 B CD 1077 E CD CD 1_555 metalc 2.847 A B GLU 18 B OE1 GLU 18 10_756 B CD 1077 E CD CD 1_555 metalc 2.337 A B ASP 21 B OD1 ASP 21 1_555 B CD 1077 E CD CD 1_555 metalc 2.574 A B ASP 21 B OD2 ASP 21 1_555 B CD 1077 E CD CD 1_555 metalc 2.391 B B ASP 21 B OD1 ASP 21 1_555 B CD 1077 E CD CD 1_555 metalc 2.877 A B LYS 29 B NZ LYS 29 1_555 B CD 1077 E CD CD 1_555 metalc 2.263 B ASP 32 B OD2 ASP 32 7_674 B CO 1079 F CO CO 1_555 metalc 2.416 B GLU 64 B OE1 GLU 64 1_555 B CO 1081 H CO CO 1_555 metalc 2.274 B HIS 68 B NE2 HIS 68 24_676 B CO 1081 H CO CO 1_555 metalc 2.709 A B CD 1077 E CD CD 1_555 B CL 1080 G CL CL 1_555 metalc 2.326 B CO 1079 F CO CO 1_555 B HOH 2047 J O HOH 1_555 metalc 1.980 B CO 1081 H CO CO 1_555 B HOH 2039 J O HOH 1_555 SIGNALING PROTEIN LYS6, LYS63, NF-KB, UBIQUITIN, NUCLEAR PROTEIN, SIGNAL TRANSDUCTION, SIGNALING PROTEIN UBIQ_HUMAN UNP 1 P62988 1 76 2JF5 1 76 P62988 A 1 1 76 1 76 2JF5 1 76 P62988 B 1 1 76 5 5 anti-parallel parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel A THR 12 A THR 12 A GLU 16 A GLU 16 A GLN 2 A GLN 2 A LYS 6 A LYS 6 A THR 66 A THR 66 A LEU 71 A LEU 71 A GLN 41 A GLN 41 A PHE 45 A PHE 45 A LYS 48 A LYS 48 A GLN 49 A GLN 49 B THR 12 B THR 12 B GLU 16 B GLU 16 B GLN 2 B GLN 2 B LYS 6 B LYS 6 B THR 66 B THR 66 B LEU 71 B LEU 71 B GLN 41 B GLN 41 B PHE 45 B PHE 45 B LYS 48 B LYS 48 B GLN 49 B GLN 49 BINDING SITE FOR RESIDUE CD B 1077 B CD 1077 Software 5 BINDING SITE FOR RESIDUE CD A 1076 A CD 1076 Software 4 BINDING SITE FOR RESIDUE CO B 1079 B CO 1079 Software 4 BINDING SITE FOR RESIDUE CL B 1080 B CL 1080 Software 3 BINDING SITE FOR RESIDUE MG A 1078 A MG 1078 Software 4 BINDING SITE FOR RESIDUE CO B 1081 B CO 1081 Software 4 B GLU 18 B GLU 18 5 10_756 B GLU 18 B GLU 18 5 1_555 B ASP 21 B ASP 21 5 1_555 B LYS 29 B LYS 29 5 1_555 B CL 1080 G CL 5 1_555 A GLU 18 A GLU 18 4 12_664 A GLU 18 A GLU 18 4 1_555 A ASP 21 A ASP 21 4 1_555 A LYS 29 A LYS 29 4 1_555 B MET 1 B MET 1 4 1_555 B GLU 16 B GLU 16 4 1_555 B ASP 32 B ASP 32 4 7_674 B HOH 2047 J HOH 4 1_555 B GLU 18 B GLU 18 3 1_555 B LYS 29 B LYS 29 3 1_555 B CD 1077 E CD 3 1_555 A MET 1 A MET 1 4 1_555 A GLU 16 A GLU 16 4 1_555 A ASP 32 A ASP 32 4 6_566 A HOH 2005 I HOH 4 1_555 B GLU 64 B GLU 64 4 1_555 B HIS 68 B HIS 68 4 24_676 B HOH 2039 J HOH 4 1_555 B HOH 2043 J HOH 4 24_676 212 P 43 3 2