6AU3

Crystal structure of SETDB1 Tudor domain with aryl triazole fragments

• PDB DOI: https://doi.org/10.2210/pdb6AU3/pdb

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


• Deposited: 2017-08-30 Released: 2017-09-27 
• Deposition Author(s): MADER, P., Mendoza-Sanchez, R., IQBAL, A., DONG, A., DOBROVETSKY, E., CORLESS, V.B., LIEW, S.K., TEMPEL, W., SMIL, D., DELA SENA, C.C., KENNEDY, S., DIAZ, D., HOLOWNIA, A., VEDADI, M., BROWN, P.J., SANTHAKUMAR, V., Bountra, C., Edwards, A.M., YUDIN, A.K., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.190 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Literature

Crystal structure of SETDB1 Tudor domain with aryl triazole fragments

MADER, P., Mendoza-Sanchez, R., IQBAL, A., DONG, A., DOBROVETSKY, E., CORLESS, V.B., LIEW, S.K., TEMPEL, W., SMIL, D., DELA SENA, C.C., KENNEDY, S., DIAZ, D., HOLOWNIA, A., VEDADI, M., BROWN, P.J., SANTHAKUMAR, V., Bountra, C., Edwards, A.M., YUDIN, A.K., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.58 kDa 
• Atom Count: 1,864 
• Modelled Residue Count: 206 
• Deposited Residue Count: 213 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETDB1	A	213	Homo sapiens	Mutation(s): 0  Gene Names: SETDB1, KIAA0067, KMT1E EC: 2.1.1.43 (PDB Primary Data), 2.1.1.366 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15047 (Homo sapiens) Explore Q15047  Go to UniProtKB:  Q15047
PHAROS:  Q15047 GTEx:  ENSG00000143379

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BWM	B [auth A]	N-{[2-(3,5-dimethyl-4H-1,2,4-triazol-4-yl)phenyl]methyl}acetamide C13 H16 N4 O FLTCDBPTYKZRMD-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding Affinity
BWM	BindingDB:  6AU3	Kd: 3.50e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.190 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.172	α = 90
b = 63.528	β = 90
c = 69.987	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): MADER, P., Mendoza-Sanchez, R., IQBAL, A., DONG, A., DOBROVETSKY, E., CORLESS, V.B., LIEW, S.K., TEMPEL, W., SMIL, D., DELA SENA, C.C., KENNEDY, S., DIAZ, D., HOLOWNIA, A., VEDADI, M., BROWN, P.J., SANTHAKUMAR, V., Bountra, C., Edwards, A.M., YUDIN, A.K., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references