6XVG

Human Sirt6 3-318 in complex with ADP-ribose and the activator MDL-801


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Binding site for activator MDL-801 on SIRT6.

You, W.Steegborn, C.

(2021) Nat Chem Biol 17: 519-521


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-6
A, B, C, D, E
A, B, C, D, E, F
316Homo sapiensMutation(s): 0 
Gene Names: SIRT6SIR2L6
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N6T7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8L9 (Subject of Investigation/LOI)
Query on 8L9

Download Ideal Coordinates CCD File 
EA [auth D]
J [auth A]
MA [auth E]
O [auth B]
SA [auth F]
EA [auth D],
J [auth A],
MA [auth E],
O [auth B],
SA [auth F],
Z [auth C]
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
Query on AR6

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BA [auth D]
G [auth A]
JA [auth E]
L [auth B]
QA [auth F]
BA [auth D],
G [auth A],
JA [auth E],
L [auth B],
QA [auth F],
V [auth C]
[(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
Query on SO4

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AA [auth C]
FA [auth D]
GA [auth D]
HA [auth D]
K [auth A]
AA [auth C],
FA [auth D],
GA [auth D],
HA [auth D],
K [auth A],
NA [auth E],
OA [auth E],
P [auth B],
PA [auth E],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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DA [auth D]
I [auth A]
IA [auth E]
LA [auth E]
N [auth B]
DA [auth D],
I [auth A],
IA [auth E],
LA [auth E],
N [auth B],
U [auth C],
X [auth C],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth D]
H [auth A]
KA [auth E]
M [auth B]
RA [auth F]
CA [auth D],
H [auth A],
KA [auth E],
M [auth B],
RA [auth F],
W [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.51α = 90
b = 136.534β = 117.71
c = 89.873γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySTE1701/15

Revision History  (Full details and data files)

  • 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