MolNFT v1 · #120289 · protein
Zebrafish USP30 in complex with LYS6-linked diubiquitin
5GVI · Ubiquitin carboxyl-terminal hydrolase 30: “Zebrafish USP30 in complex with LYS6-linked diubiquitin”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.70). MolNFT v1 #120289 on GenesisL1: 3D structure, binding sites…
- PDB
- 5GVI
- Type
- protein
- Length
- 474 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 30; Ubiquitin
- UniProt
- A0A0R4ILB8, P62983
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 30 | protein | 326 | 25% helix, 33% strand | A0A0R4ILB8 |
| B | Ubiquitin | protein | 76 | 24% helix, 32% strand | P62983 |
| C | Ubiquitin | protein | 72 | 25% helix, 36% strand | P62983 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.70 | 0.98 | 25 | empty |
| 2 | 345 | 0.55 | 0.75 | 40 | empty |
| 3 | 70 | 0.44 | 0.82 | 18 | empty |
| 4 | 69 | 0.41 | 0.80 | 16 | empty |
| 5 | 128 | 0.41 | 0.75 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1940 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 534 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 58 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 5GVI · Zebrafish USP30 in complex with Lys6-linked diubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- P62983 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62983) · a predicted model of the same protein · chain C 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 A0A0R4ILB8
- Every structure of UniProt P62983
- Elsewhere: RCSB PDB 5GVI · PDBe 5GVI · UniProt A0A0R4ILB8 · UniProt P62983
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.