6RLL | pdb_00006rll

CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ44064146

• PDB DOI: https://doi.org/10.2210/pdb6RLL/pdb

• Classification: TRANSLOCASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
• Mutation(s): No 


• Deposited: 2019-05-02 Released: 2020-06-03 
• Deposition Author(s): Brown, D.G., Robinson, C.M., Pande, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Literature

A chemical probe for the methyl transferase PRMT5 with a novel binding mode

Brown, D.G., Robinson, C.M., Pandeet, V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.74 kDa 
• Atom Count: 7,408 
• Modelled Residue Count: 928 
• Deposited Residue Count: 993 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 5	A	645	Homo sapiens	Mutation(s): 0  Gene Names: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 EC: 2.1.1.320
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens) Explore O14744  Go to UniProtKB:  O14744
PHAROS:  O14744 GTEx:  ENSG00000100462

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylosome protein 50	B	348	Homo sapiens	Mutation(s): 0  Gene Names: WDR77, MEP50, WD45, HKMT1069, Nbla10071
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA1 (Homo sapiens) Explore Q9BQA1  Go to UniProtKB:  Q9BQA1
PHAROS:  Q9BQA1 GTEx:  ENSG00000116455

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K8H (Subject of Investigation/LOI)	C [auth A]	(2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)-5-(1,8-diazaspiro[4.5]decan-1-ylmethyl)oxolane-3,4-diol C19 H28 N6 O3 RERIOYBALRXMSF-ATNYBXOESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
K8H	BindingDB:  6RLL	IC50: min: 9.5, max: 58 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.956	α = 90
b = 136.048	β = 90
c = 179.298	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Brown, D.G., Robinson, C.M., Pande, V.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description