MolNFT v1 · #75245 · protein

Human SIRT6 crystal structure in complex with 2'-N-acetyl ADP ribose

3PKJ · NAD-dependent deacetylase sirtuin-6: “Human SIRT6 crystal structure in complex with 2'-N-acetyl ADP ribose”. X-ray diffraction, 4 ligands (A2N, ZN, UNX), 18 pockets (best druggability 0.85). MolNFT v1 #75245 on GenesisL1: 3D…

PDB: 3PKJ
Type: protein
Length: 1,664 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: A2N, ZN, UNX, SO4
Pockets: 18 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 30% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-)	protein	277	30% helix, 16% strand	Q8N6T7
B	NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-)	protein	280	30% helix, 16% strand	Q8N6T7
C	NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-)	protein	276	31% helix, 16% strand	Q8N6T7
D	NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-)	protein	276	32% helix, 16% strand	Q8N6T7
E	NAD-dependent deacetylase sirtuin-6 (EC 3.5.1.-)	protein	278	30% helix, 15% strand	Q8N6T7

Ligands and binding sites

A2N · [(2R,3S,4R,5R)-4-(acetylamino)-3,5-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 6 copies · chains A, B, E, C, D, F
ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
UNX · Unknown atom or ion · ion · 35 copies · chains A, F, B, C, D, E
SO4 · Sulfate ion · ion · 12 copies · chains A, B, E, C, D, 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1067	0.85	0.86	125	A2N, SO4
2	528	0.75	0.82	60	A2N
3	539	0.75	0.82	56	A2N, SO4
4	548	0.74	0.82	57	A2N
5	600	0.74	0.81	61	A2N, SO4

Interfaces

9 interfaces between chains.

B–E · 1077 Å² buried · 11 hydrogen bonds · protein-protein
A–F · 583 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 345 Å² buried · 1 hydrogen bond · protein-protein
A–B · 300 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 242 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3PKJ · Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose · 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 3PKJ · PDBe 3PKJ · UniProt Q8N6T7

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