MolNFT v1 · #129414 · protein
Sirtuin 5 from danio rerio in complex with 3-hydroxy-3-methylglutaryl- CPS1 peptide
5OJO · NAD-dependent protein deacylase sirtuin-5, mitochondrial: “Sirtuin 5 from danio rerio in complex with 3-hydroxy-3-methylglutaryl- CPS1 peptide”. X-ray diffraction, 2 ligands (ZN, NA), 7 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 5OJO
- Type
- protein
- Length
- 538 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase sirtuin-5, mitochondrial; Carbamoyl-phosphate synthase…
- EC
- 3.5.1.-, 6.3.4.16
- UniProt
- Q6DHI5, P31327
- Ligands
- ZN, NA
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 265 | 36% helix, 19% strand | Q6DHI5 |
| C | Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16) | protein | 8 | 50% helix, 13% strand | P31327 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- DMS · Dimethyl sulfoxide · additive · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, C
- 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
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 | 333 | 0.69 | 0.82 | 30 | EPE |
| 2 | 169 | 0.57 | 0.81 | 32 | EDO |
| 3 | 222 | 0.53 | 0.77 | 20 | empty |
| 4 | 165 | 0.48 | 0.77 | 21 | empty |
| 5 | 58 | 0.31 | 0.76 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 661 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 613 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5OJO · Sirtuin 5 from Danio rerio in complex with 3-hydroxy-3-methylglutaryl-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 0.93
- P31327 · AlphaFold monomer V2.0 prediction for carbamoyl-phosphate synthase [ammonia]… · a predicted model of the same protein · chain C against A, TM-score 0.42
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 P31327
- Elsewhere: RCSB PDB 5OJO · PDBe 5OJO · UniProt Q6DHI5 · UniProt P31327
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