Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 38676.62 
• Atom Count: 2537 
• Residue Count: 325 
• Unique protein chains: 2

5Y2F

Human SIRT6 in complex with allosteric activator MDL-801

• DOI: 10.2210/pdb5Y2F/pdb

• Classification: HYDROLASE/PEPTIDE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2017-07-25 Released: 2018-11-07 
• Deposition Author(s): Zhang, J., Huang, Z., Song, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.217 
• R-Value Work: 0.175 

Literature

Identification of a cellularly active SIRT6 allosteric activator.

Huang, Z., Zhao, J., Deng, W., Chen, Y., Shang, J., Song, K., Zhang, L., Wang, C., Lu, S., Yang, X., He, B., Min, J., Hu, H., Tan, M., Xu, J., Zhang, Q., Zhong, J., Sun, X., Mao, Z., Lin, H., Xiao, M., Chin, Y.E., Jiang, H., Xu, Y., Chen, G., Zhang, J.

(2018) Nat. Chem. Biol. 14: 1118-1126

• PubMed: 30374165 

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NAD-dependent protein deacetylase sirtuin-6	A	316	Homo sapiens	Mutation(s): 0  Gene Names: SIRT6 (SIR2L6) EC: 3.5.1.-
Find proteins for Q8N6T7 (Homo sapiens) Go to Gene View: SIRT6 Go to UniProtKB:  Q8N6T7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
9-mer peptide QTARKSTGG	C	9	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
8L9	A	5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid C20 H14 Br Cl2 F N2 O6 S2 MJYYUGUIBHEWRX-UHFFFAOYSA-N
HDR	C	HEXADECANE-1-SULFINIC ACID C16 H34 O2 S HBTBNXFVJYRYGI-UHFFFAOYSA-N
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
AR6	A	[(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 C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.217 
• R-Value Work: 0.175 
• Space Group: P 4₁ 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 162.422	α = 90.00
b = 162.422	β = 90.00
c = 162.422	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data processing
PHASER	phasing
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-07-25 
• Released Date: 2018-11-07 
• Deposition Author(s): Zhang, J., Huang, Z., Song, K.

Revision History 

• Version 1.0: 2018-11-07
  Type: Initial release
• Version 1.1: 2018-11-14
  Type: Data collection, Database references
• Version 1.2: 2018-11-28
  Type: Data collection, Database references