7CL0

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.248
R-Value Work: 0.206
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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

Organizational Affiliation

Department of Pathophysiology, Shanghai Jiaotong University School of Medicine, Shanghai, China.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N6T7 (Homo sapiens) Explore Q8N6T7 Go to UniProtKB: Q8N6T7
PHAROS: Q8N6T7 GTEx: ENSG00000077463
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N6T7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AR6 Query on AR6 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
G4U Query on G4U Download Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D]	U [auth D]	tetradecanethial C₁₄ H₂₈ S JIHBDFISBDNMMA-UHFFFAOYSA-N		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D]	V [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A]	M [auth A] N [auth A] O [auth A] P [auth A] Q [auth A] 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		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.248
R-Value Work: 0.206
R-Value Observed: 0.208
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-02-24

Deposition Author(s):

Song, K.

Zhang, J.

Revision History (Full details and data files)

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