Research workbench
Crystal structure of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester
Analyse Crystal structure of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KW5
- 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 | 38% 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 | 50 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1212 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3KW5 · Crystal structure of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin… · 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 3KW5 · PDBe 3KW5 · UniProt P09936 · UniProt P62988
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