5ISA

Crystal structure of mouse CARM1 in complex with inhibitor SA0401

PDB DOI: https://doi.org/10.2210/pdb5ISA/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2016-03-15 Released: 2017-03-15
Deposition Author(s): Cura, V., Marechal, N., Mailliot, J., Troffer-Charlier, N., Hassenboehler, P., Wurtz, J.M., Bonnefond, L., Cavarelli, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.204
R-Value Work: 0.161
R-Value Observed: 0.163

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of mouse CARM1 in complex with inhibitor SA0401

Cura, V., Marechal, N., Mailliot, J., Troffer-Charlier, N., Wurtz, J.M., Bonnefond, L., Cavarelli, J.

To be published.

Macromolecule Content

Total Structure Weight: 167.98 kDa
Atom Count: 11,558
Modelled Residue Count: 1,372
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-arginine methyltransferase CARM1	A [auth C], B [auth D], C [auth A], D [auth B]	364	Mus musculus	Mutation(s): 0 Gene Names: Carm1, Prmt4 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q9WVG6 (Mus musculus) Explore Q9WVG6 Go to UniProtKB: Q9WVG6
IMPC: MGI:1913208
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WVG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6D5 Query on 6D5 Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain J [auth D] SDF format, chain M [auth A] SDF format, chain S [auth B] MOL2 format, chain E [auth C] MOL2 format, chain J [auth D] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] mmCIF format, chain E [auth C] mmCIF format, chain J [auth D] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B]	E [auth C], J [auth D], M [auth A], S [auth B]	(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azidopropyl)amino]-2-azanyl-butanoic acid C₁₇ H₂₆ N₁₀ O₅ HOYYGMYIDDINNM-UOYPZJKHSA-N		Interactions Focus chain E [auth C] Focus chain J [auth D] Focus chain M [auth A] Focus chain S [auth B] Interactions & Density Focus chain E [auth C] Focus chain J [auth D] Focus chain M [auth A] Focus chain S [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
M2M Query on M2M Download Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	1-METHOXY-2-(2-METHOXYETHOXY)ETHANE C₆ H₁₄ O₃ SBZXBUIDTXKZTM-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
DXE Query on DXE Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain P [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain P [auth A] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain P [auth A]	H [auth C], I [auth C], P [auth A]	1,2-DIMETHOXYETHANE C₄ H₁₀ O₂ XTHFKEDIFFGKHM-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain I [auth C] Focus chain P [auth A] Interactions & Density Focus chain H [auth C] Focus chain I [auth C] Focus chain P [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	F [auth C] G [auth C] K [auth D] L [auth D] N [auth A] F [auth C], G [auth C], K [auth D], L [auth D], N [auth A], O [auth A], T [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Focus chain G [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth C] Focus chain G [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.204
R-Value Work: 0.161
R-Value Observed: 0.163
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.541	α = 90
b = 98.409	β = 90
c = 205.803	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-03-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-15
Type: Initial release
Version 2.0: 2018-03-07
Changes: Atomic model, Non-polymer description, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description