MolNFT v1 · #148941 · protein
Crystal structure of zebrafish sirtuin 5 in complex with 3(S)- (NAPHTHYLTHIO)SUCCINYL-CPS1 peptide
6FLG · NAD-dependent protein deacylase sirtuin-5, mitochondrial: “Crystal structure of zebrafish sirtuin 5 in complex with 3(S)- (NAPHTHYLTHIO)SUCCINYL-CPS1 peptide”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.72).…
- PDB
- 6FLG
- Type
- protein
- Length
- 538 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase sirtuin-5, mitochondrial…
- EC
- 3.5.1.-
- UniProt
- Q6DHI5
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 264 | 35% helix, 18% strand | Q6DHI5 |
| B | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 266 | 33% helix, 18% strand | Q6DHI5 |
| C | 3(S)-(NAPHTHYLTHIO)SUCCINYL-CPS1 peptide | protein | 8 | 50% helix, 13% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains 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 | 342 | 0.72 | 0.84 | 30 | EPE, EDO |
| 2 | 251 | 0.59 | 0.79 | 35 | empty |
| 3 | 201 | 0.50 | 0.76 | 21 | empty |
| 4 | 159 | 0.48 | 0.77 | 20 | empty |
| 5 | 59 | 0.35 | 0.78 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–C · 736 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 646 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6FLG · Crystal structure of zebrafish Sirtuin 5 in complex with 3(S)-(naphthylthio)succinyl-CPS1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6DHI5 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase sirtuin-5… · a predicted model of the same protein · chain B 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 Q6DHI5
- Elsewhere: RCSB PDB 6FLG · PDBe 6FLG · UniProt Q6DHI5
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