6HOY

Human Sirt6 in complex with ADP-ribose and the inhibitor trichostatin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Sirtuin 6 Inhibition by the Hydroxamate Trichostatin A: Implications for Protein Deacylase Drug Development.

You, W.Steegborn, C.

(2018) J.Med.Chem. 61: 10922-10928


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-6
A, B
302Homo sapiensMutation(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
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TSN
Query on TSN

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Download CCD File 
A, B
TRICHOSTATIN A
7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE
C17 H22 N2 O3
RTKIYFITIVXBLE-QEQCGCAPSA-N
 Ligand Interaction
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
AR6
Query on AR6

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Download CCD File 
A, 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.154 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 91.291α = 90.00
b = 91.291β = 90.00
c = 143.681γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-09-18 
  • Released Date: 2018-11-14 
  • Deposition Author(s): You, W., Steegborn, C.

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references