8SHB

Crystal Structure of PRMT3 with Compound YD1-208

• PDB DOI: https://doi.org/10.2210/pdb8SHB/pdb

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


• Deposited: 2023-04-13 Released: 2024-04-24 
• Deposition Author(s): Song, X., Dong, A., Deng, Y., Huang, R., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.238 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Crystal Structure of PRMT3 with Compound YD1-208

Song, X., Dong, A., Deng, Y., Huang, R., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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)

Macromolecule Content

• Total Structure Weight: 38.74 kDa 
• Atom Count: 2,473 
• Modelled Residue Count: 302 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 3	A	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
GV3 (Subject of Investigation/LOI)	B [auth A]	5'-S-[3-(N'-phenylcarbamimidamido)propyl]-5'-thioadenosine C20 H26 N8 O3 S PAOYFGCZLHEXFB-NVQRDWNXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.238 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M38SHB

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.14	α = 90
b = 70.14	β = 90
c = 172.37	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Song, X., Dong, A., Deng, Y., Huang, R., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Other private	Canada	--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release