Research workbench
Crystal structure of zebrafish Sirtuin 5 in complex with adipoylated CPS1-peptide
Analyse Crystal structure of zebrafish Sirtuin 5 in complex with adipoylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UTZ
- Type
- protein
- Length
- 531 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- DANIO RERIO; SYNTHETIC CONSTRUCT
- Molecule
- Sirtuin 5; Carbamoylphosphate synthetase I
- EC
- 3.5.1.-
- UniProt
- Q6DHI5, Q5R209
- Ligands
- 0L1, ZN, NA
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · resolution 3.3 · 3 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sirtuin 5 (EC 3.5.1.-) | protein | 262 | 37% helix, 20% strand | Q6DHI5 |
| B | Sirtuin 5 (EC 3.5.1.-) | protein | 261 | 38% helix, 20% strand | Q6DHI5 |
| D | Carbamoylphosphate synthetase I | protein | 8 | 38% helix, 13% strand | Q5R209 |
Ligands and binding sites
- 0L1 · hexanedioic acid · ligand · chains A, D
- 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
- DMS · Dimethyl sulfoxide · additive · chains A, B
- EDO · 1,2-ethanediol · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.71 | 0.86 | 40 | 0L1 |
| 2 | 331 | 0.71 | 0.83 | 29 | EPE, EDO |
| 3 | 229 | 0.55 | 0.78 | 33 | DMS |
| 4 | 173 | 0.53 | 0.79 | 27 | empty |
| 5 | 66 | 0.36 | 0.77 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 656 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 470 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4UTZ · Crystal structure of zebrafish sirtuin 5 in complex with adipoylated CPS1-peptide · 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
- Every structure of UniProt Q5R209
- Elsewhere: RCSB PDB 4UTZ · PDBe 4UTZ · UniProt Q6DHI5 · UniProt Q5R209
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