Research workbench
Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog
Analyse Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I5I
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-1
- EC
- 3.5.1.-
- UniProt
- Q96EB6
- Ligands
- 4I5, NAD, ZN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent protein deacetylase sirtuin-1 (EC 3.5.1.-) | protein | 272 | 36% helix, 18% strand | Q96EB6 |
Ligands and binding sites
- 4I5 · (6S)-2-chloro-5,6,7,8,9,10-hexahydrocyclohepta[b]indole-6-carboxamide · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.81 | 0.88 | 61 | 4I5, NAD |
| 2 | 481 | 0.81 | 0.88 | 62 | 4I5, NAD |
| 3 | 712 | 0.68 | 0.76 | 92 | empty |
| 4 | 110 | 0.51 | 0.82 | 31 | empty |
| 5 | 51 | 0.26 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1057 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4I5I · Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog · the same entry in another collection · chain A against A, TM-score 1.00
- Q96EB6 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-1 (Q96EB6) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q96EB6
- Elsewhere: RCSB PDB 4I5I · PDBe 4I5I · UniProt Q96EB6
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