Research workbench
Crystal structure of human amsh-lp dub domain in complex with LYS63- linked ubiquitin dimer
Analyse Crystal structure of human amsh-lp dub domain in complex with LYS63- linked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZNV
- Type
- protein
- Length
- 640 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amsh-like protease; Ubiquitin
- EC
- 3.1.2.15
- UniProt
- Q96FJ0, P62991
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Amsh-like protease (EC 3.1.2.15) | protein | 172 | 27% helix, 35% strand | Q96FJ0 |
| B, E | Ubiquitin | protein | 76 | 24% helix, 36% strand | P62991 |
| C | Ubiquitin | protein | 77 | 25% helix, 27% strand | P62991 |
| F | Ubiquitin | protein | 67 | 27% helix, 31% strand | P62991 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.78 | 0.86 | 70 | EDO |
| 2 | 863 | 0.70 | 0.76 | 81 | EDO |
| 3 | 139 | 0.51 | 0.79 | 23 | empty |
| 4 | 127 | 0.50 | 0.80 | 33 | empty |
| 5 | 118 | 0.45 | 0.78 | 23 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1338 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1337 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 523 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 487 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 471 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 2ZNV · Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer · the same entry in another collection · chain C against C, TM-score 1.00
- Q96FJ0 · AlphaFold monomer V2.0 prediction for amsh-like protease (Q96FJ0) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q96FJ0
- Every structure of UniProt P62991
- Elsewhere: RCSB PDB 2ZNV · PDBe 2ZNV · UniProt Q96FJ0 · UniProt P62991
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