Research workbench
Crystal structure of human SIRT5 in complex with the fluorogenic tetrapeptide substrate P15
Analyse Crystal structure of human SIRT5 in complex with the fluorogenic tetrapeptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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