2ZNV: Human AMSH-LP DUB domain
Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer. Determined by X-ray diffraction at 1.6 Å resolution. Released 2 Sept 2008.
- Method
- X-ray diffraction
- Resolution
- 1.6 Å
- Organisms
- Homo sapiens, Mus musculus
- Chains
- 6
- Atoms
- 5,691
- Mol. weight
- 74.74 kDa
- Ligands
- ZN
- Released
- 2 Sept 2008
Explore 2ZNV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
2ZNV contains 29 α-helices and 52 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 6 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 266-268 | 3 | |
| β-strand | 269-272 | 4 | 1 |
| α-helix | 275-287 | 13 | |
| β-strand | 294-302 | 9 | 1 |
| β-strand | 305-313 | 9 | 1 |
| β-strand | 316-318 | 3 | 2 |
| β-strand | 323-325 | 3 | 2 |
| α-helix | 329-337 | 9 | |
| β-strand | 341-348 | 8 | 1 |
| α-helix | 358-370 | 13 | |
| β-strand | 375-380 | 6 | 1 |
| α-helix | 381-383 | 3 | |
| β-strand | 385-391 | 7 | 1 |
| α-helix | 393-401 | 9 | |
| β-strand | 417-419 | 3 | 1 |
| β-strand | 423-426 | 4 | 1 |
| β-strand | 431-434 | 4 | 1 |
Chain B: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 3 |
| β-strand | 12-16 | 5 | 3 |
| β-strand | 22 | 1 | 4 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 3 |
| β-strand | 48-49 | 2 | 3 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 4 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 3 |
| β-strand | 74-75 | 2 | 2 |
Chain C: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 5 |
| β-strand | 12-16 | 5 | 5 |
| β-strand | 22 | 1 | 6 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 43-45 | 3 | 5 |
| β-strand | 48-49 | 2 | 5 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 6 |
| α-helix | 56-59 | 4 | |
| β-strand | 66-69 | 4 | 5 |
| α-helix | 71-73 | 3 | |
Chain D: 7 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 266-268 | 3 | |
| β-strand | 269-272 | 4 | 7 |
| α-helix | 275-287 | 13 | |
| β-strand | 294-302 | 9 | 7 |
| β-strand | 305-313 | 9 | 7 |
| β-strand | 316-318 | 3 | 8 |
| β-strand | 323-325 | 3 | 8 |
| α-helix | 329-338 | 10 | |
| α-helix | 340 | 1 | |
| β-strand | 341-348 | 8 | 7 |
| α-helix | 358-370 | 13 | |
| β-strand | 375-380 | 6 | 7 |
| α-helix | 381-383 | 3 | |
| β-strand | 385-391 | 7 | 7 |
| α-helix | 393-400 | 8 | |
| β-strand | 417-419 | 3 | 7 |
| β-strand | 423-426 | 4 | 7 |
| β-strand | 431-434 | 4 | 7 |
Chain E: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 9 |
| β-strand | 12-16 | 5 | 9 |
| β-strand | 22 | 1 | 10 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 9 |
| β-strand | 48-49 | 2 | 9 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 10 |
| β-strand | 66-71 | 6 | 9 |
| β-strand | 74-75 | 2 | 8 |
Chain F: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 11 |
| β-strand | 12-16 | 5 | 11 |
| β-strand | 22 | 1 | 12 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 43-45 | 3 | 11 |
| β-strand | 48-49 | 2 | 11 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 12 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-69 | 4 | 11 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| AMSH-like protease | A, D | protein | 178 | Homo sapiens | Q96FJ0 (AlphaFold model) |
| Ubiquitin | B, E | protein | 76 | Mus musculus | P0CG50 (AlphaFold model) |
| Ubiquitin | C, F | protein | 77 | Mus musculus | P0CG50 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>2ZNV_1 AMSH-like protease (chains A, D)
GPGHMEGLRCVVLPEDLCHKFLQLAESNTVRGIATCGILCGKLTHNEFTITHVIVPKQSA
GPDYCDMENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIV
CSPKHKDTGIFRLTNAGMLEVSACKKKGFHPHTKEPRLFSICKHVLVKDIKIIVLDLR
Sequence of entity 2 (B, E), FASTA
>2ZNV_2 Ubiquitin (chains B, E)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQRESTLHLVLRLRGG
Sequence of entity 3 (C, F), FASTA
>2ZNV_3 Ubiquitin (chains C, F)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Water and common crystallization additives (EDO) are not listed.
Primary citation
Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains. Sato, Y., Yoshikawa, A., Yamagata, A. et al. Nature (2008) 455:358-362. DOI 10.1038/nature07254 · PubMed
Other PDB entries of the same protein (UniProt Q96FJ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2ZNR 1.2 Å, Crystal structure of the DUB domain of human AMSH-LP
- 7L97 2.01 Å, Crystal structure of STAMBPL1 in complex with an engineered binder
Browse structure collections
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