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Crystal structure of AL3 PHD finger bound to H3K4me3

Analyse Crystal structure of AL3 PHD finger bound to H3K4me3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YC4
Type: protein
Length: 69 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.697
Source: Arabidopsis thaliana; SYNTHETIC CONSTRUCT
Molecule: PHD finger protein ALFIN-LIKE 3; Histone H3K4me3
UniProt: Q9M2B4
Ligands: ZN

Structure

x-ray diffraction · resolution 2.697 · 2 distinct chains · 6% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PHD finger protein ALFIN-LIKE 3	protein	60	7% helix, 13% strand	Q9M2B4
P	Histone H3K4me3	protein	9	0% helix, 44% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A

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

Interfaces

1 interface between chains.

A–P · 620 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (methylation).

Compared structures

5YC4 · Crystal structure of AL3 phd finger bound to H3K4ME3 · the same entry in another collection · chain A against A, TM-score 1.00
Q9M2B4 · AlphaFold monomer V2.0 prediction for phd finger protein alfin-like 3 (Q9M2B4) · a predicted model of the same protein · chain A against A, TM-score 0.82

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 Q9M2B4
Elsewhere: RCSB PDB 5YC4 · PDBe 5YC4 · UniProt Q9M2B4

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