MolNFT v1 · #96467 · protein
Crystal structure of the S18Y variant of ubiquitin carboxy-terminal hydrolase L1
4JKJ · Ubiquitin carboxyl-terminal hydrolase isozyme L1: “Crystal structure of the S18Y variant of ubiquitin carboxy-terminal hydrolase L1”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.53). MolNFT v1 #96467 on…
- PDB
- 4JKJ
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase isozyme L1
- EC
- 3.4.19.12
- UniProt
- P09936
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12) | protein | 223 | 38% helix, 21% strand | P09936 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.53 | 0.83 | 27 | SO4 |
| 2 | 143 | 0.49 | 0.78 | 26 | SO4 |
| 3 | 133 | 0.42 | 0.75 | 22 | empty |
| 4 | 55 | 0.31 | 0.76 | 12 | empty |
| 5 | 50 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 595 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4JKJ · Crystal Structure of the S18Y Variant of Ubiquitin Carboxy-terminal Hydrolase L1 · 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
- Elsewhere: RCSB PDB 4JKJ · PDBe 4JKJ · UniProt P09936
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.