MolNFT v1 · #77553 · protein
SIRT5 is an NAD-dependent protein lysine demalonylase and desuccinylase
3RIG · NAD-dependent deacetylase sirtuin-5: “SIRT5 is an NAD-dependent protein lysine demalonylase and desuccinylase”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.64). MolNFT v1 #77553 on GenesisL1: 3D structure…
- PDB
- 3RIG
- Type
- protein
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase sirtuin-5; Peptide of histone 3 thioacetyl-lysine 9
- EC
- 3.5.1.-
- UniProt
- Q9NXA8
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase sirtuin-5 (EC 3.5.1.-) | protein | 260 | 37% helix, 20% strand | Q9NXA8 |
| B | NAD-dependent deacetylase sirtuin-5 (EC 3.5.1.-) | protein | 258 | 37% helix, 21% strand | Q9NXA8 |
| C, D | Peptide of histone 3 thioacetyl-lysine 9 | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.64 | 0.78 | 48 | NHE |
| 2 | 271 | 0.60 | 0.79 | 31 | NHE |
| 3 | 90 | 0.38 | 0.77 | 17 | empty |
| 4 | 67 | 0.38 | 0.79 | 25 | empty |
| 5 | 62 | 0.32 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 539 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 518 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 516 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 3RIG · Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NXA8 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase sirtuin-5… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9NXA8
- Elsewhere: RCSB PDB 3RIG · PDBe 3RIG · UniProt Q9NXA8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.