6XV1 | pdb_00006xv1

Human Sirt6 13-308 in complex with ADP-ribose and the activator MDL-801

• PDB DOI: https://doi.org/10.2210/pdb6XV1/pdb

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


• Deposited: 2020-01-21 Released: 2020-10-28 
• Deposition Author(s): You, W., Steegborn, C.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Binding site for activator MDL-801 on SIRT6.

You, W., Steegborn, C.

(2021) Nat Chem Biol 17: 519-521

• PubMed: 33649599 
• DOI: https://doi.org/10.1038/s41589-021-00749-y
• Primary Citation Related Structures: 
  6XUY, 6XV1, 6XV6, 6XVG

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Organizational Affiliation: 
• Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
Department of Biochemistry, University of Bayreuth, Bayreuth, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.89 kDa 
• Atom Count: 4,595 
• Modeled Residue Count: 559 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-6	A, B	302	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8L9 (Subject of Investigation/LOI)	E [auth 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
AR6	C [auth A], K [auth B]	[(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
SO4	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8L9	BindingDB:  6XV1	EC50: min: 5700, max: 1.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.175	α = 90
b = 91.175	β = 90
c = 143.584	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-28 
Deposition Author(s): You, W., Steegborn, C.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	STE1701/15

Revision History  

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2021-03-17
  Changes: Database references
• Version 1.2: 2021-05-05
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description