6SQ3 | pdb_00006sq3

Crystal structure of mouse PRMT6 in complex with inhibitor U1

PDB DOI: https://doi.org/10.2210/pdb6SQ3/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-09-03 Released: 2020-09-30
Deposition Author(s): Bonnefond, L., Cavarelli, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.295 (Depositor), 0.306 (DCC)
R-Value Work:
0.251 (Depositor), 0.261 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of mouse PRMT6 in complex with inhibitors

Bonnefond, L., Cavarelli, J.

To be published.

Macromolecule Content

Total Structure Weight: 86.29 kDa
Atom Count: 5,095
Modeled Residue Count: 641
Deposited Residue Count: 772
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 6	A, B	386	Mus musculus	Mutation(s): 1 Gene Names: Prmt6, Hrmt1l6 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NZB1 (Mus musculus) Explore Q6NZB1 Go to UniProtKB: Q6NZB1
IMPC: MGI:2139971
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NZB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6RE (Subject of Investigation/LOI) Query on 6RE Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	[[2-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethylamino]-azanyl-methylidene]azanium C₁₂ H₁₉ N₈ O₃ OIGRVZYOOMUALG-IOSLPCCCSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.295 (Depositor), 0.306 (DCC)
R-Value Work: 0.251 (Depositor), 0.261 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.526	α = 90
b = 117.979	β = 103.3
c = 71.945	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-09-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-09-30
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.