MolNFT v1 · #106017 · protein
Human SIRT2 in complex with SIRREAL1 and ac-lys-otc peptide
4RMI · NAD-dependent protein deacetylase sirtuin-2: “Human SIRT2 in complex with SIRREAL1 and ac-lys-otc peptide”. X-ray diffraction, 2 ligands (3TK, ZN), 2 pockets (best druggability 0.76). MolNFT v1 #106017 on GenesisL1: 3D structure…
- PDB
- 4RMI
- Type
- protein
- Length
- 281 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-2; Ac-lys-otc peptide
- EC
- 3.5.1.-
- UniProt
- Q8IXJ6
- Ligands
- 3TK, ZN
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 278 | 37% helix, 18% strand | Q8IXJ6 |
| B | Ac-lys-otc peptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 3TK · N-(5-benzyl-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.76 | 0.84 | 55 | 3TK |
| 2 | 97 | 0.35 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 393 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 4RMI · Human Sirt2 in complex with SirReal1 and Ac-Lys-OTC 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 0.97
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 4RMI · PDBe 4RMI · UniProt Q8IXJ6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.