MolNFT v1 · #69605 · protein
Crystal structure of the I93M mutant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester
3KVF · Ubiquitin carboxyl-terminal hydrolase isozyme L1: “Crystal structure of the I93M mutant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin…”. X-ray diffraction, 1 ligand (GVE), 1 pocket (best druggability 0.30). MolNFT v1…
- PDB
- 3KVF
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase isozyme L1; Ubiquitin
- EC
- 3.4.19.12, 6.-.-.-
- UniProt
- P09936, P62988
- Ligands
- GVE
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12, 6.-.-.-) | protein | 223 | 37% helix, 20% strand | P09936 |
| B | Ubiquitin | protein | 75 | 24% helix, 36% strand | P62988 |
Ligands and binding sites
- GVE · Methyl 4-aminobutanoate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.30 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1178 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3KVF · Crystal structure of the I93M mutant of ubiquitin carboxy terminal hydrolase L1 bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- P09936 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase isozyme L1… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P09936
- Every structure of UniProt P62988
- Elsewhere: RCSB PDB 3KVF · PDBe 3KVF · UniProt P09936 · UniProt P62988
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