MolNFT v1 · #108022 · protein
Crystal structure of zebrafish sirtuin 5 in complex with 3, 3-dimethyl-succinylated CPS1-peptide
4UU8 · NAD-dependent protein deacylase sirtuin-5, mitochondrial: “Crystal structure of zebrafish sirtuin 5 in complex with 3, 3-dimethyl-succinylated CPS1-peptide”. X-ray diffraction, 4 ligands (BEZ, WOC, ZN), 6 pockets (best druggability…
- PDB
- 4UU8
- Type
- protein
- Length
- 536 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, WOC, ZN, NA
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 262 | 37% helix, 19% strand | Q6DHI5 |
| B | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 266 | 36% helix, 18% strand | Q6DHI5 |
| D | Carbamoylphosphate synthetase I | protein | 8 | 50% helix, 13% strand | Q5R209 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains D
- WOC · 2,2-dimethylbutanedioic acid · ligand · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- DMS · Dimethyl sulfoxide · additive · chains A, 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.73 | 0.89 | 29 | WOC |
| 2 | 299 | 0.71 | 0.84 | 29 | EPE, EDO |
| 3 | 198 | 0.51 | 0.77 | 28 | DMS |
| 4 | 181 | 0.49 | 0.77 | 20 | empty |
| 5 | 59 | 0.31 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 647 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 486 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4UU8 · Crystal structure of zebrafish Sirtuin 5 in complex with 3,3-dimethyl- 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 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
- Every structure of UniProt Q5R209
- Elsewhere: RCSB PDB 4UU8 · PDBe 4UU8 · UniProt Q6DHI5 · UniProt Q5R209
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