7CL0 | pdb_00007cl0

Crystal structure of human SIRT6

• PDB DOI: https://doi.org/10.2210/pdb7CL0/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-20 Released: 2021-02-24 
• Deposition Author(s): Song, K., Zhang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 
  0.248 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Reply to: Binding site for MDL-801 on SIRT6.

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., Shen, H., Xu, Y., Chen, G., Zhang, J.

(2021) Nat Chem Biol 17: 522-523

• PubMed: 33649600 
• DOI: https://doi.org/10.1038/s41589-021-00750-5
• Primary Citation Related Structures: 
  7CL0, 7CL1

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Organizational Affiliation: 
• Department of Pathophysiology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guizhou Medical University, Guiyang, China.
Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
School of Life Sciences and Technology, Tongji University, Shanghai, China.
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
Ailewei Company, Shanghai, China.
Department of Pathophysiology, Shanghai Jiaotong University School of Medicine, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.31 kDa 
• Atom Count: 2,710 
• Modeled Residue Count: 301 
• Deposited Residue Count: 364 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-6	A	355	Homo sapiens	Mutation(s): 0  Gene Names: SIRT6, SIR2L6 EC: 2.3.1.286 (PDB Primary Data), 2.4.2 (UniProt), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N6T7 (Homo sapiens) Explore Q8N6T7  Go to UniProtKB:  Q8N6T7
PHAROS:  Q8N6T7 GTEx:  ENSG00000077463

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THR-ALA-ARG-LYS-SER-THR-GLY	B [auth D]	9	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6	C [auth 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
G4U	U [auth D]	tetradecanethial C14 H28 S JIHBDFISBDNMMA-UHFFFAOYSA-N
PEG	V [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free:  0.248 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.795	α = 90
b = 161.795	β = 90
c = 161.795	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-24 
Deposition Author(s): Song, K., Zhang, J.

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release
  
• Version 1.1: 2021-03-24
  Changes: Database references
• Version 1.2: 2021-05-12
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary