6BPI | pdb_00006bpi

Crystal structure of SETDB1 Tudor domain with aryl triazole fragment peptide conjugates

• PDB DOI: https://doi.org/10.2210/pdb6BPI/pdb

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


• Deposited: 2017-11-23 Released: 2017-12-27 
• Deposition Author(s): MADER, P., Mendoza-Sanchez, R., DONG, A., DOBROVETSKY, E., IQBAL, A., CORLESS, V., TEMPEL, W., LIEW, S.K., SMIL, D., DELA SENA, C.C., KENNEDY, S., DIAZ, D.B., SCHAPIRA, M., VEDADI, M., BROWN, P.J., Santhakumar, V., FRYE, S., 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: 1.64 Å
• R-Value Free: 
  0.199 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of SETDB1 Tudor domain with aryl triazole fragment peptide conjugates

MADER, P., Mendoza-Sanchez, R., DONG, A., DOBROVETSKY, E., IQBAL, A., CORLESS, V., TEMPEL, W., LIEW, S.K., SMIL, D., DELA SENA, C.C., KENNEDY, S., DIAZ, D.B., SCHAPIRA, M., VEDADI, M., BROWN, P.J., Santhakumar, V., FRYE, S., 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: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 26.13 kDa 
• Atom Count: 2,059 
• Modeled Residue Count: 211 
• Deposited Residue Count: 217 
• Unique protein chains: 2

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MLY-SER-THR-E2G	B	4	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX	J [auth A], K [auth A], L [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
E2G	B	PEPTIDE-LIKE	C15 H20 N6 O3		--
MLY	B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.199 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36BPI

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.731	α = 90
b = 63.756	β = 90
c = 69.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): MADER, P., Mendoza-Sanchez, R., DONG, A., DOBROVETSKY, E., IQBAL, A., CORLESS, V., TEMPEL, W., LIEW, S.K., SMIL, D., DELA SENA, C.C., KENNEDY, S., DIAZ, D.B., SCHAPIRA, M., VEDADI, M., BROWN, P.J., Santhakumar, V., FRYE, S., Bountra, C., Edwards, A.M., YUDIN, A.K., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Structure summary