6RLQ

CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ45031882

PDB DOI: https://doi.org/10.2210/pdb6RLQ/pdb

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

Deposited: 2019-05-02 Released: 2020-07-15
Deposition Author(s): Brown, D.G., Robinson, C.M., Pande, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.299
R-Value Work: 0.230
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ45031882

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

To be published.

Macromolecule Content

Total Structure Weight: 111.7 kDa
Atom Count: 7,351
Modelled Residue Count: 928
Deposited Residue Count: 992
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 5	A	644	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) Go to UniProtKB: O14744
PHAROS: O14744 GTEx: ENSG00000100462
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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) Go to UniProtKB: Q9BQA1
PHAROS: Q9BQA1 GTEx: ENSG00000116455
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K8N (Subject of Investigation/LOI) Query on K8N Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(1~{S},2~{R},3~{S},5~{R})-3-[2-(2-azanyl-3-bromanyl-quinolin-7-yl)ethyl]-5-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)cyclop entane-1,2-diol C₂₂ H₂₃ Br N₆ O₂ DBSMLQTUDJVICQ-CJODITQLSA-N		Interactions Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
K8N	BindingDB: 6RLQ	IC50: min: 0.13, max: 6.3 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.299
R-Value Work: 0.230
R-Value Observed: 0.233
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.132	α = 90
b = 137.854	β = 90
c = 178.617	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-15
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.