MolNFT v1 · #155421 · protein
Sirtuin 2 demyristoylation native intermediate I & II mixture
6L71 · NAD-dependent protein deacetylase sirtuin-2: “Sirtuin 2 demyristoylation native intermediate I & II mixture”. X-ray diffraction, 3 ligands (NCA, YOY, YDD), 3 pockets (best druggability 0.84). MolNFT v1 #155421 on GenesisL1: 3D…
- PDB
- 6L71
- Type
- protein
- Length
- 302 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-2; Pro-arg-lys-gln-leu-ala
- EC
- 2.3.1.286
- UniProt
- Q8IXJ6
- Ligands
- NCA, YOY, YDD
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 2.3.1.286) | protein | 296 | 37% helix, 17% strand | Q8IXJ6 |
| C | Pro-arg-lys-gln-leu-ala | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- NCA · Nicotinamide · ligand · chains A
- YOY · [[(2S,3aS,5S,6R,6aS)-2-dodecyl-6-oxidanyl-3a,5,6,6a-tetrahydrofuro[2,3-d][1,3]dioxol-5-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · chains A, C
- YDD · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.84 | 0.92 | 53 | NCA, YOY, YDD |
| 2 | 134 | 0.41 | 0.75 | 27 | empty |
| 3 | 55 | 0.26 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–C · 473 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6L71 · Sirtuin 2 demyristoylation native intermediate I & II mixture · the same entry in another collection · chain C against C, TM-score 1.00
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 Q8IXJ6
- Elsewhere: RCSB PDB 6L71 · PDBe 6L71 · UniProt Q8IXJ6
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