Research workbench
Crystal structure of zebrafish sirtuin 5 in complex with 3-phenyl- succinylated CPS1-peptide
Analyse Crystal structure of zebrafish sirtuin 5 in complex with 3-phenyl- succinylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UTV
- Type
- protein
- Length
- 524 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase sirtuin-5, mitochondrial; Carbamoylphosphate synthetase I
- EC
- 3.5.1.-
- UniProt
- Q6DHI5, Q5R209
- Ligands
- BEZ, FSL, F9V, ZN, NA
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 257 | 38% helix, 19% strand | Q6DHI5 |
| B | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 259 | 37% helix, 19% strand | Q6DHI5 |
| C | Carbamoylphosphate synthetase I | protein | 8 | 50% helix, 13% strand | Q5R209 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains A, C
- FSL · (2R)-2-phenylbutanedioic acid · ligand · chains A, C
- F9V · (2S)-2-phenylbutanedioic acid · ligand · chains A, C
- 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.68 | 0.86 | 33 | FSL, F9V |
| 2 | 330 | 0.68 | 0.82 | 31 | EPE |
| 3 | 216 | 0.55 | 0.79 | 25 | DMS |
| 4 | 151 | 0.45 | 0.76 | 19 | empty |
| 5 | 63 | 0.37 | 0.78 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 657 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4UTV · Crystal structure of zebrafish Sirtuin 5 in complex with 3-phenyl- succinylated… · 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
- Every structure of UniProt Q5R209
- Elsewhere: RCSB PDB 4UTV · PDBe 4UTV · UniProt Q6DHI5 · UniProt Q5R209
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