6DVR

Crystal structure of human CARM1 with (R)-SKI-72

• PDB DOI: https://doi.org/10.2210/pdb6DVR/pdb

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


• Deposited: 2018-06-25 Released: 2018-07-25 
• Deposition Author(s): Dong, A., Zeng, H., Hutchinson, A., Seitova, A., Luo, M., Cai, X.C., Ke, W., Wang, J., Shi, C., Zheng, W., Lee, J.P., Ibanez, G., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.215 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Literature

Crystal structure of human CARM1 with (R)-SKI-72

Zeng, H., Dong, A., Hutchinson, A., Seitova, A., Luo, M., Cai, X.C., Ke, W., Wang, J., Shi, C., Zheng, W., Lee, J.P., Ibanez, G., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.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 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.78 kDa 
• Atom Count: 6,056 
• Modelled Residue Count: 667 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-arginine methyltransferase CARM1	A, B	344	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HDG	C [auth A], I [auth B]	(2R,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-[(benzylamino)methyl]-N-[2-(4-methoxyphenyl)ethyl]hexanamide (non-preferred name) C32 H42 N8 O5 ZLHYSNFCYFOANJ-DVTMEHRLSA-N
P15	D [auth A], J [auth B]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C13 H28 O7 FHHGCKHKTAJLOM-UHFFFAOYSA-N
UNX	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.215 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.366	α = 90
b = 98.579	β = 90
c = 207.375	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Dong, A., Zeng, H., Hutchinson, A., Seitova, A., Luo, M., Cai, X.C., Ke, W., Wang, J., Shi, C., Zheng, W., Lee, J.P., Ibanez, G., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description