Research workbench

Crystal structure of human SIRT6

Analyse Crystal structure of human SIRT6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3K35
Type: protein
Length: 1,654 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: APR, ZN, UNX, SO4
Pockets: 18 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 31% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-)	protein	274	30% helix, 16% strand	Q8N6T7
B, E	NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-)	protein	276	31% helix, 16% strand	Q8N6T7
C	NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-)	protein	275	31% helix, 16% strand	Q8N6T7
D	NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-)	protein	273	31% helix, 18% strand	Q8N6T7
F	NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-)	protein	280	31% helix, 16% strand	Q8N6T7

Ligands and binding sites

APR · Adenosine-5-diphosphoribose · ligand · 6 copies · chains A, B, C, D, E, F
ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
UNX · Unknown atom or ion · ion · 18 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 13 copies · chains A, B, D, C, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1159	0.77	0.79	102	APR, SO4, UNX
2	556	0.75	0.82	57	APR, SO4, UNX
3	621	0.74	0.81	69	APR, UNX
4	548	0.74	0.82	54	APR, UNX
5	539	0.73	0.81	56	APR, UNX

Interfaces

7 interfaces between chains.

B–D · 578 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 477 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 399 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 303 Å² buried · 2 hydrogen bonds · protein-protein
A–E · 263 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3K35 · Crystal Structure of Human SIRT6 · 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 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 3K35 · PDBe 3K35 · UniProt Q8N6T7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.