Research workbench
Human SIRT6 in complex with allosteric activator mdl-801 (3.2A)
Analyse Human SIRT6 in complex with allosteric activator mdl-801 (3.2A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CL1
- Type
- protein
- Length
- 304 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-6; Thr-ala-arg-lys-ser-thr-gly-gly
- EC
- 2.3.1.286
- UniProt
- Q8N6T7
- Ligands
- AR6, 8L9, G4X, ZN, SO4
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 296 | 29% helix, 15% strand | Q8N6T7 |
| C | Thr-ala-arg-lys-ser-thr-gly-gly | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · chains A, C
- 8L9 · 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid · ligand · chains A
- G4X · hexadecanethial · ligand · chains A, C
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.81 | 0.88 | 60 | AR6, G4X |
| 2 | 182 | 0.54 | 0.79 | 32 | GOL |
| 3 | 51 | 0.30 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–C · 545 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7CL1 · Human SIRT6 in complex with allosteric activator MDL-801 (3.2A) · the same entry in another collection · chain A against A, 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 Q8N6T7
- Elsewhere: RCSB PDB 7CL1 · PDBe 7CL1 · UniProt Q8N6T7
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