5MF6

Human Sirt6 in complex with activator UBCS039


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 5MF6

Classification: HYDROLASE

Total Structure Weight: 70112.11

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-dependent protein deacetylase sirtuin-6 A, B 302 Homo sapiens EC#: 3.5.1 IUBMB
Mutation: G8I, L9D, S10P, P11F, Y12T
Gene Name(s): SIRT6 Gene View SIR2L6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AR6
Query on AR6

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 Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
7M2
Query on 7M2

A, B (4~{R})-4-pyridin-3-yl-4,5-dihydropyrrolo[1,2- a]quinoxaline
C16 H13 N3
BSOBGTYXYGHUTD-MRXNPFEDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

A TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.190
  • Space Group: P 63

Unit Cell:

Length (Å) Angle (°)
a = 91.30 α = 90.00
b = 91.30 β = 90.00
c = 144.32 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-11-17
  • Released Date: 2016-12-28
  • Deposition author(s): Steegborn, C., You, W., Kambach, C.

Revision History

  • 2017-01-25
    Type: Database references