Research workbench
SIRT5 is an NAD-dependent protein lysine demalonylase and desuccinylase
Analyse SIRT5 is an NAD-dependent protein lysine demalonylase and desuccinylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RIY
- Type
- protein
- Length
- 559 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 N-succinyl lysine 9
- EC
- 3.5.1.-
- UniProt
- Q9NXA8
- Ligands
- NAD, ZN
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent deacetylase sirtuin-5 (EC 3.5.1.-) | protein | 272 | 39% helix, 20% strand | Q9NXA8 |
| C | Peptide of histone 3 N-succinyl lysine 9 | protein | 7 | 0% helix, 43% strand | — |
| D | Peptide of histone 3 N-succinyl lysine 9 | protein | 8 | 0% helix, 38% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, D, B, C
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.74 | 0.85 | 52 | NAD |
| 2 | 333 | 0.73 | 0.85 | 51 | NAD |
| 3 | 98 | 0.38 | 0.76 | 19 | empty |
| 4 | 78 | 0.35 | 0.76 | 17 | empty |
| 5 | 71 | 0.33 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 617 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 601 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 544 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 3RIY · 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 3RIY · PDBe 3RIY · UniProt Q9NXA8
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