MolNFT v1 · #114667 · protein
Crystal structure of SIRT5 in complex with a coumarin-labelled succinyl peptide
5BWL · NAD-dependent protein deacylase sirtuin-5, mitochondrial: “Crystal structure of SIRT5 in complex with a coumarin-labelled succinyl peptide”. X-ray diffraction, 2 ligands (MCM, ZN), 2 pockets (best druggability 0.57). MolNFT v1…
- PDB
- 5BWL
- Type
- protein
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase sirtuin-5, mitochondrial; Coumarin-labelled succinyl…
- EC
- 3.5.1.-
- UniProt
- Q9NXA8
- Ligands
- MCM, ZN
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 267 | 36% helix, 19% strand | Q9NXA8 |
| B | Coumarin-labelled succinyl peptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
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 | 115 | 0.57 | 0.84 | 29 | MCM |
| 2 | 73 | 0.33 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 440 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 5BWL · Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide · 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 0.95
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 5BWL · PDBe 5BWL · UniProt Q9NXA8
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