8TE4

Crystal structure of the methyltransferase domain of R882H/N879A DNMT3A homotetramer

PDB DOI: https://doi.org/10.2210/pdb8TE4/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-07-05 Released: 2024-03-13
Deposition Author(s): Lu, J.W., Song, J.K.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.236
R-Value Work: 0.203
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the methyltransferase domain of R882H/N879A DNMT3A homotetramer

Lu, J.W., Song, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 265.39 kDa
Atom Count: 14,869
Modelled Residue Count: 1,761
Deposited Residue Count: 2,296
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3A	A B C D [auth E] E [auth H] A, B, C, D [auth E], E [auth H], F, G [auth D], H [auth G]	287	Homo sapiens	Mutation(s): 2 Gene Names: DNMT3A EC: 2.1.1.37 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K1 (Homo sapiens) Explore Q9Y6K1 Go to UniProtKB: Q9Y6K1
PHAROS: Q9Y6K1 GTEx: ENSG00000119772
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y6K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain X [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D]	I [auth A], O [auth B], U [auth C], X [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain X [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain L [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] J [auth A] K [auth A] L [auth A] AA [auth D], BA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], V [auth C], W [auth C], Y [auth D], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D]