4QBR | pdb_00004qbr

Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide

PDB DOI: https://doi.org/10.2210/pdb4QBR/pdb

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

Deposited: 2014-05-08 Released: 2015-05-13
Deposition Author(s): Wang, H., Li, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.225 (Depositor), 0.223 (DCC)
R-Value Work:
0.178 (Depositor), 0.183 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4QBR

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

Literature

Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs

Noh, K., Wang, H., Kim, H., Wenderski, W., Fang, F., Li, C., Dewell, S., Wu, X., Ferris, A., Hughes, S.H., Zheng, D., Melnick, A.M., Patel, D.J., Li, H., Allis, C.D.

To be published.

Macromolecule Content

Total Structure Weight: 33.3 kDa
Atom Count: 2,486
Modeled Residue Count: 286
Deposited Residue Count: 288
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3A	A, C	137	Homo sapiens	Mutation(s): 1 Gene Names: DNMT3A EC: 2.1.1.37 (PDB Primary Data), 2.1.1 (UniProt)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y6K1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	B [auth P], D [auth E]	7	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431 GTEx: ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775
Entity Groups
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C]	E [auth A] F [auth A] G [auth A] H [auth C] I [auth C] E [auth A], F [auth A], G [auth A], H [auth C], I [auth C], J [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.225 (Depositor), 0.223 (DCC)
R-Value Work: 0.178 (Depositor), 0.183 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.057	α = 78.7
b = 37.161	β = 83.89
c = 50.125	γ = 81.56

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-05-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-13
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.