8SIH | pdb_00008sih

Crystal Structure of PRMT4 with Compound YD1-289

• PDB DOI: https://doi.org/10.2210/pdb8SIH/pdb

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


• Deposited: 2023-04-16 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: 2.35 Å
• R-Value Free: 
  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of PRMT4 with Compound YD1-289

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: 41.64 kDa 
• Atom Count: 2,764 
• Modeled Residue Count: 331 
• Deposited Residue Count: 359 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-arginine methyltransferase CARM1	A	359	Homo sapiens	Mutation(s): 0  Gene Names: CARM1, PRMT4 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q86X55 (Homo sapiens) Explore Q86X55  Go to UniProtKB:  Q86X55
PHAROS:  Q86X55 GTEx:  ENSG00000142453

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I1K (Subject of Investigation/LOI)	B [auth A]	5'-{[2-(benzylcarbamamido)ethyl][3-(N'-cyclopentylcarbamimidamido)propyl]amino}-5'-deoxyadenosine C29 H43 N11 O4 BGNWKEZAKOEUDI-VBHAUSMQSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38SIH

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.582	α = 90
b = 86.582	β = 90
c = 136.026	γ = 120

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		--

Revision History  

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