MolNFT v1 · #110771 · protein
Human SIRT2 in complex with 2-O-myristoyl-ADP-ribose
4Y6Q · NAD-dependent protein deacetylase sirtuin-2: “Human SIRT2 in complex with 2-O-myristoyl-ADP-ribose”. X-ray diffraction, 2 ligands (OMR, ZN), 14 pockets (best druggability 0.87). MolNFT v1 #110771 on GenesisL1: 3D structure, binding…
- PDB
- 4Y6Q
- Type
- protein
- Length
- 1,132 residues
- Chains
- 4
- 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
- OMR, ZN
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 287 | 39% helix, 17% strand | Q8IXJ6 |
| C | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 286 | 40% helix, 17% strand | Q8IXJ6 |
| D | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 272 | 39% helix, 18% strand | Q8IXJ6 |
Ligands and binding sites
- OMR · [(2S,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] tetradecanoate · ligand · 4 copies · chains A, D, B, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.87 | 0.88 | 103 | OMR |
| 2 | 482 | 0.84 | 0.90 | 56 | OMR |
| 3 | 1086 | 0.83 | 0.84 | 90 | OMR |
| 4 | 794 | 0.81 | 0.84 | 80 | OMR |
| 5 | 841 | 0.77 | 0.81 | 76 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1187 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1054 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 315 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 294 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 203 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4Y6Q · Human SIRT2 in complex with 2-O-myristoyl-ADP-ribose · 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 C against A, TM-score 0.98
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 4Y6Q · PDBe 4Y6Q · UniProt Q8IXJ6
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