MolNFT v1 · #155823 · protein
Crystal structure of human SIRT5 in complex with the fluorogenic tetrapeptide substrate P15
6LJN · NAD-dependent protein deacylase sirtuin-5, mitochondrial: “Crystal structure of human SIRT5 in complex with the fluorogenic tetrapeptide substrate P15”. X-ray diffraction, 2 ligands (MCM, ZN), 2 pockets (best druggability 0.70).…
- PDB
- 6LJN
- Type
- protein
- Length
- 271 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase sirtuin-5, mitochondrial; His-phe-ser-lys
- EC
- 2.3.1.-
- UniProt
- Q9NXA8
- Ligands
- MCM, ZN
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 2.3.1.-) | protein | 267 | 37% helix, 19% strand | Q9NXA8 |
| B | His-phe-ser-lys | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- MCM · 7-amino-4-methyl-chromen-2-one · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
- SIN · Succinic acid · additive · chains A, B
- ACY · Acetic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.70 | 0.89 | 32 | SIN |
| 2 | 68 | 0.33 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 376 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct, covalent ligand).
Compared structures
- 6LJN · Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate… · 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 0.94
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 6LJN · PDBe 6LJN · UniProt Q9NXA8
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