MolNFT v1 · #75244 · protein
Human SIRT6 crystal structure in complex with ADP ribose
3PKI · NAD-dependent deacetylase sirtuin-6: “Human SIRT6 crystal structure in complex with ADP ribose”. X-ray diffraction, 4 ligands (AR6, ZN, UNX), 20 pockets (best druggability 0.85). MolNFT v1 #75244 on GenesisL1: 3D structure, binding…
- PDB
- 3PKI
- Type
- protein
- Length
- 1,671 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase sirtuin-6
- EC
- 3.5.1.-
- UniProt
- Q8N6T7
- Ligands
- AR6, ZN, UNX, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-) | protein | 285 | 29% helix, 19% strand | Q8N6T7 |
| B, E | NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-) | protein | 276 | 31% helix, 18% strand | Q8N6T7 |
| C | NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-) | protein | 277 | 30% helix, 18% strand | Q8N6T7 |
| D | NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-) | protein | 283 | 29% helix, 18% strand | Q8N6T7 |
| F | NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-) | protein | 274 | 31% helix, 19% strand | Q8N6T7 |
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 · 6 copies · chains A, E, B, F, C, D
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- UNX · Unknown atom or ion · ion · 26 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 23 copies · chains A, B, E, C, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.85 | 0.86 | 122 | UNX, AR6, SO4 |
| 2 | 1091 | 0.84 | 0.85 | 128 | AR6, SO4, UNX |
| 3 | 460 | 0.76 | 0.84 | 53 | AR6, UNX |
| 4 | 436 | 0.76 | 0.85 | 54 | AR6, UNX |
| 5 | 87 | 0.73 | 0.96 | 23 | SO4 |
Interfaces
10 interfaces between chains.
- B–F · 1116 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1110 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1096 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 844 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 733 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3PKI · Human SIRT6 crystal structure in complex with ADP ribose · the same entry in another collection · chain F against F, TM-score 1.00
- Q8N6T7 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-6 (Q8N6T7) · a predicted model of the same protein · chain C 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 3PKI · PDBe 3PKI · UniProt Q8N6T7
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