5Y2F

Human SIRT6 in complex with allosteric activator MDL-801


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-6
A
316Homo 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
9-mer peptide QTARKSTGG
C
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
8L9
Query on 8L9

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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
 Ligand Interaction
HDR
Query on HDR

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C
HEXADECANE-1-SULFINIC ACID
C16 H34 O2 S
HBTBNXFVJYRYGI-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
AR6
Query on AR6

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Download CCD File 
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
 Ligand Interaction
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 = 162.422α = 90.00
b = 162.422β = 90.00
c = 162.422γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
HKL-3000data processing
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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