8T68 | pdb_00008t68

Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1 in complex with RQ3-111

• PDB DOI: https://doi.org/10.2210/pdb8T68/pdb

• Classification: TRANSPORT PROTEIN,TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-15 Released: 2024-11-27 
• Deposition Author(s): Zeng, H., Dong, A., Brown, P.J., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1 in complex with RQ3-111.

Zeng, H., Dong, A., Brown, P.J., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.48 kDa 
• Atom Count: 1,968 
• Modeled Residue Count: 232 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase KMT5B	A	274	Homo sapiens	Mutation(s): 0  Gene Names: KMT5B, SUV420H1, CGI-85 EC: 2.1.1.362 (PDB Primary Data), 2.1.1.361 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q4FZB7 (Homo sapiens) Explore Q4FZB7  Go to UniProtKB:  Q4FZB7
PHAROS:  Q4FZB7 GTEx:  ENSG00000110066

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZKI (Subject of Investigation/LOI)	D [auth A]	6,7-dichloro-N-[(3R)-oxolan-3-yl]-4-(pyridin-4-yl)phthalazin-1-amine C17 H14 Cl2 N4 O VPPZBKRTEZMHNH-LLVKDONJSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38T68

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.149	α = 90
b = 75.528	β = 90
c = 96.807	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Zeng, H., Dong, A., Brown, P.J., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release