Research workbench
Human SIRT2 crystal structure in complex with BHJH-TM1
Analyse Human SIRT2 crystal structure in complex with BHJH-TM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R8M
- Type
- protein
- Length
- 581 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- NAD-dependent protein deacetylase sirtuin-2; BHJH-TM1 peptide
- EC
- 3.5.1.-
- UniProt
- Q8IXJ6
- Ligands
- 3LX, ZN
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.1 · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 286 | 38% helix, 18% strand | Q8IXJ6 |
| B | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 285 | 40% helix, 18% strand | Q8IXJ6 |
| C, D | BHJH-TM1 peptide | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- 3LX · tridecanethial · ligand · 2 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.81 | 0.89 | 46 | 3LX |
| 2 | 951 | 0.80 | 0.82 | 88 | 3LX |
| 3 | 109 | 0.39 | 0.75 | 20 | empty |
| 4 | 103 | 0.37 | 0.75 | 19 | empty |
| 5 | 54 | 0.29 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 404 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 398 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4R8M · Human SIRT2 crystal structure in complex with bhjh-TM1 · 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 4R8M · PDBe 4R8M · UniProt Q8IXJ6
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