8HFP

Crystal structure of the methyl-CpG-binding domain of SETDB2 in complex with the cysteine-rich domain of C11orf46 protein

PDB DOI: https://doi.org/10.2210/pdb8HFP/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-11-11 Released: 2023-11-22
Deposition Author(s): Mahana, Y., Ariyoshi, M., Shirakawa, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.227
R-Value Work: 0.186
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

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

Literature

Structural Evidence for Protein Binding by the Methyl-CpG-Binding Domain of SETDB Proteins

Mahana, Y., Ariyoshi, M., Nagao, K., Obuse, C., Shirakawa, M.

To be published.

Macromolecule Content

Total Structure Weight: 42.93 kDa
Atom Count: 2,568
Modelled Residue Count: 306
Deposited Residue Count: 370
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARL14 effector protein	A, C [auth B]	77	Homo sapiens	Mutation(s): 0 Gene Names: ARL14EP, ARF7EP, C11orf46
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N8R7 (Homo sapiens) Explore Q8N8R7 Go to UniProtKB: Q8N8R7
PHAROS: Q8N8R7 GTEx: ENSG00000152219
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N8R7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETDB2	B [auth C], D	108	Homo sapiens	Mutation(s): 0 Gene Names: SETDB2, C13orf4, CLLD8, KMT1F EC: 2.1.1.366
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T68 (Homo sapiens) Explore Q96T68 Go to UniProtKB: Q96T68
PHAROS: Q96T68 GTEx: ENSG00000136169
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96T68
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth D]	G [auth A] I [auth C] J [auth C] M [auth B] N [auth B] G [auth A], I [auth C], J [auth C], M [auth B], N [auth B], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth C] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth D]	E [auth A] F [auth A] H [auth C] K [auth B] L [auth B] E [auth A], F [auth A], H [auth C], K [auth B], L [auth B], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth D]