7BJ1

Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site

• PDB DOI: https://doi.org/10.2210/pdb7BJ1/pdb
• Entry: 7BJ1 supersedes: 6Z2R

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-01-13 Released: 2021-03-03 
• Deposition Author(s): Talibov, V.O., Cederfelt, D., Dobritzsch, D., Danielson, U.H.
• Funding Organization(s): Swedish Research Council, Italian Association for Cancer Research

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.210 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase

Talibov, V.O., Fabini, E., FitzGerald, E.A., Tedesco, D., Cederfeldt, D., Talu, M.J., Rachman, M.M., Mihalic, F., Manoni, E., Naldi, M., Sanese, P., Forte, G., Barril, X., Simone, C., Bartolini, M., Dobritzsch, D., Danielson, U.H.

(2021) Chembiochem 22: 1597-1608

• DOI: https://doi.org/10.1002/cbic.202000736

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 50.75 kDa 
• Atom Count: 4,048 
• Modelled Residue Count: 426 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SMYD3	A	431	Homo sapiens	Mutation(s): 2  Gene Names: SMYD3, ZMYND1, ZNFN3A1 EC: 2.1.1.354
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens) Explore Q9H7B4  Go to UniProtKB:  Q9H7B4
PHAROS:  Q9H7B4 GTEx:  ENSG00000185420

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
QKT (Subject of Investigation/LOI)	C [auth A]	Diperodon (S-enantiomer) C22 H27 N3 O4 YUGZHQHSNYIFLG-FQEVSTJZSA-N
GOL	I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	G [auth A], H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.210 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.909	α = 90
b = 66.05	β = 90
c = 107.277	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Talibov, V.O., Cederfelt, D., Dobritzsch, D., Danielson, U.H.
• This entry supersedes: 6Z2R

---

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	D0571301
Italian Association for Cancer Research	Italy	19172

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Advisory
• Version 1.2: 2021-03-17
  Changes: Advisory
• Version 1.3: 2021-10-06
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2024-01-31
  Changes: Data collection, Refinement description