8SHR | pdb_00008shr

Crystal Structure of PRMT3 with Compound YD1-214

• PDB DOI: https://doi.org/10.2210/pdb8SHR/pdb

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


• Deposited: 2023-04-14 Released: 2024-04-17 
• 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: 1.92 Å
• R-Value Free: 
  0.215 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of PRMT3 with Compound YD1-214

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: 38.73 kDa 
• Atom Count: 2,574 
• Modeled Residue Count: 311 
• 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
HIY (Subject of Investigation/LOI)	B [auth A]	5'-S-[2-(phenylcarbamamido)ethyl]-5'-thioadenosine C19 H23 N7 O4 S ZVEFVGBDFYZLDZ-SCFUHWHPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.215 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38SHR

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.211	α = 90
b = 70.211	β = 90
c = 175.142	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
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: 2024-04-17
  Type: Initial release