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Crystal structure of SDG8 cw domain in complex with H3K4ME1 peptide

Analyse Crystal structure of SDG8 cw domain in complex with H3K4ME1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YVX
Type: protein
Length: 67 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-lysine N-methyltransferase ASHH2; H3K4ME1
EC: 2.1.1.43
UniProt: Q2LAE1
Ligands: ZN

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone-lysine N-methyltransferase ASHH2 (EC 2.1.1.43)	protein	60	25% helix, 17% strand	Q2LAE1
C	H3K4ME1	protein	7	0% helix, 29% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

A–C · 594 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (methylation).

Compared structures

5YVX · Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q2LAE1 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase ASHH2 (Q2LAE1) · a predicted model of the same protein · chain A against A, TM-score 0.89

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q2LAE1
Elsewhere: RCSB PDB 5YVX · PDBe 5YVX · UniProt Q2LAE1

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