MolNFT v1 · #148925 · protein
Crystal structure of zebrafish sirtuin 5 in complex with 3- (BENZYLTHIO)SUCCINYL-CPS1 peptide
6FKY · NAD-dependent protein deacylase sirtuin-5, mitochondrial: “Crystal structure of zebrafish sirtuin 5 in complex with 3- (BENZYLTHIO)SUCCINYL-CPS1 peptide”. X-ray diffraction, 4 ligands (E9N, DZK, ZN), 8 pockets (best druggability…
- PDB
- 6FKY
- Type
- protein
- Length
- 544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase sirtuin-5, mitochondrial; 3(R)-(PHENYLTHIO)SUCCINYL-CPS1…
- EC
- 3.5.1.-
- UniProt
- Q6DHI5
- Ligands
- E9N, DZK, ZN, NA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 262 | 36% helix, 19% strand | Q6DHI5 |
| B | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 266 | 37% helix, 18% strand | Q6DHI5 |
| C, I | 3(R)-(PHENYLTHIO)SUCCINYL-CPS1 peptide | protein | 8 | 0% helix, 75% strand | — |
Ligands and binding sites
- E9N · (2~{R})-2-(phenylmethylsulfanyl)butanedioic acid · ligand · chains A, C, I
- DZK · (2~{S})-2-(phenylmethylsulfanyl)butanedioic acid · ligand · chains A, C, I
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.75 | 0.96 | 25 | E9N, DZK |
| 2 | 288 | 0.67 | 0.82 | 31 | EPE, EDO |
| 3 | 225 | 0.54 | 0.78 | 25 | empty |
| 4 | 155 | 0.48 | 0.77 | 26 | empty |
| 5 | 61 | 0.32 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 642 Ų buried · 6 hydrogen bonds · protein-protein
- C–I · 616 Ų buried · 57 hydrogen bonds · protein-protein
- A–I · 532 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 6FKY · Crystal structure of zebrafish Sirtuin 5 in complex with 3-(benzylthio)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 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 Q6DHI5
- Elsewhere: RCSB PDB 6FKY · PDBe 6FKY · UniProt Q6DHI5
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