MolNFT v1 · #106016 · protein
Human SIRT2 in complex with SIRREAL2 and ac-lys-H3 peptide
4RMH · NAD-dependent protein deacetylase sirtuin-2: “Human SIRT2 in complex with SIRREAL2 and ac-lys-H3 peptide”. X-ray diffraction, 3 ligands (ALY, 3TE, ZN), 3 pockets (best druggability 0.75). MolNFT v1 #106016 on GenesisL1: 3D…
- PDB
- 4RMH
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-2
- EC
- 3.5.1.-
- UniProt
- Q8IXJ6
- Ligands
- ALY, 3TE, ZN
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 292 | 38% helix, 17% strand | Q8IXJ6 |
Ligands and binding sites
- ALY · N(6)-acetyllysine · ligand · chains A
- 3TE · 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
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 | 384 | 0.75 | 0.85 | 39 | ALY, 3TE |
| 2 | 79 | 0.39 | 0.78 | 19 | empty |
| 3 | 117 | 0.38 | 0.74 | 25 | empty |
Compared structures
- 4RMH · Human Sirt2 in complex with SirReal2 and Ac-Lys-H3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IXJ6 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-2 (Q8IXJ6) · 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 Q8IXJ6
- Elsewhere: RCSB PDB 4RMH · PDBe 4RMH · UniProt Q8IXJ6
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