8SIO

Crystal structure of PRMT3 with YD1-66

• PDB DOI: https://doi.org/10.2210/pdb8SIO/pdb

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


• Deposited: 2023-04-16 Released: 2024-04-17 
• Deposition Author(s): Song, X., Dong, A., Arrowsmith, C.H., Edwards, A.M., Deng, Y., Huang, R., Min, J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Crystal structure of PRMT3 with YD1-66

Song, X., Dong, A., Arrowsmith, C.H., Edwards, A.M., Deng, Y., Huang, R., Min, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 77.7 kDa 
• Atom Count: 4,772 
• Modelled Residue Count: 602 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 3	A, B	340	Homo sapiens	Mutation(s): 0  Gene Names: PRMT3, HRMT1L3 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for O60678 (Homo sapiens) Explore O60678  Go to UniProtKB:  O60678
PHAROS:  O60678 GTEx:  ENSG00000185238

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GXF (Subject of Investigation/LOI)	C [auth A], D [auth B]	5'-S-{3-[N'-(4'-chloro[1,1'-biphenyl]-3-yl)carbamimidamido]propyl}-5'-thioadenosine C26 H29 Cl N8 O3 S CEYIEWVKCKYWPH-PTGPVQHPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/M38SIO

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.039	α = 90
b = 100.782	β = 90
c = 173.437	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Song, X., Dong, A., Arrowsmith, C.H., Edwards, A.M., Deng, Y., Huang, R., Min, J.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release