5LKJ | pdb_00005lkj

Crystal structure of mouse CARM1 in complex with ligand SA684

PDB DOI: https://doi.org/10.2210/pdb5LKJ/pdb

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

Deposited: 2016-07-22 Released: 2017-08-16
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: 2.60 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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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 mouse CARM1 in complex with ligands

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

To be published.

Macromolecule Content

Total Structure Weight: 171.34 kDa
Atom Count: 11,635
Modeled Residue Count: 1,408
Deposited Residue Count: 1,484
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, B, C, D	371	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6YB Query on 6YB Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	E [auth A], N [auth B], U [auth C], Y [auth D]	(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-carbamimidamidoethyl)amino]-2-azanyl-butanoic acid C₁₇ H₂₈ N₁₀ O₅ JNOBHECZYPSIIL-OPYVMVOTSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain N [auth B] Focus chain U [auth C] Focus chain Y [auth D]
P33 Query on P33 Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain M [auth A] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain M [auth A] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	M [auth A], W [auth C], X [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain M [auth A] Focus chain W [auth C] Focus chain X [auth C]
DXE Query on DXE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	J [auth A], K [auth A], L [auth A], S [auth B], T [auth B]	1,2-DIMETHOXYETHANE C₄ H₁₀ O₂ XTHFKEDIFFGKHM-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C]	F [auth A] G [auth A] H [auth A] I [auth A] O [auth B] F [auth A], G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], Q [auth B], V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.637	α = 90
b = 98.161	β = 90
c = 206.499	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: 2017-08-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-08-16
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary