Research workbench
Crystal structure of zebrafish sirtuin 5 in complex with 3- (PHENYLTHIO)SUCCINYL-CPS1 peptide
Analyse Crystal structure of zebrafish sirtuin 5 in complex with 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FKZ
- Type
- protein
- Length
- 546 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase sirtuin-5, mitochondrial; 3(S)-(PHENYLTHIO)SUCCINYL-CPS1…
- EC
- 3.5.1.-
- UniProt
- Q6DHI5
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 264 | 37% helix, 19% strand | Q6DHI5 |
| B | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 266 | 38% helix, 18% strand | Q6DHI5 |
| E, H | 3(S)-(PHENYLTHIO)SUCCINYL-CPS1 peptide | protein | 8 | 0% helix, 75% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- 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
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.67 | 0.81 | 35 | EPE |
| 2 | 226 | 0.53 | 0.77 | 24 | empty |
| 3 | 138 | 0.46 | 0.77 | 20 | empty |
| 4 | 80 | 0.40 | 0.78 | 19 | GOL |
| 5 | 64 | 0.38 | 0.79 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–E · 696 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 686 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 641 Ų buried · 7 hydrogen bonds · protein-protein
- E–H · 601 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6FKZ · Crystal structure of zebrafish Sirtuin 5 in complex with 3-(phenylthio)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 0.94
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 6FKZ · PDBe 6FKZ · UniProt Q6DHI5
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