MolNFT v1 · #154449 · protein
Structure of deubiquitinase
6KBE · Ubiquitin thioesterase: “Structure of deubiquitinase”. X-ray diffraction, 4 pockets (best druggability 0.59). MolNFT v1 #154449 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KBE
- Type
- protein
- Length
- 389 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase; Polyubiquitin-C
- EC
- 3.4.19.12
- UniProt
- B9G207, P0CG48
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ubiquitin thioesterase (EC 3.4.19.12) | protein | 239 | 56% helix, 16% strand | B9G207 |
| G | Polyubiquitin-C | protein | 150 | 22% helix, 35% strand | P0CG48 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.59 | 0.81 | 31 | empty |
| 2 | 124 | 0.50 | 0.80 | 18 | empty |
| 3 | 84 | 0.39 | 0.78 | 16 | empty |
| 4 | 87 | 0.37 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- B–G · 1823 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 d-amino (D-amino acid).
Compared structures
- 6KBE · Structure of Deubiquitinase · the same entry in another collection · chain B against B, TM-score 1.00
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 B9G207
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6KBE · PDBe 6KBE · UniProt B9G207 · UniProt P0CG48
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