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Structural analysis of phd domain of pygopus complexed with trimethylated histone H3 peptide

Analyse Structural analysis of phd domain of pygopus complexed with trimethylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YYR
Type: protein
Length: 126 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pygopus homolog 1; H3K4ME3 peptide
UniProt: Q9D0P5
Ligands: ZN

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pygopus homolog 1	protein	60	28% helix, 18% strand	Q9D0P5
P	H3K4ME3 peptide	protein	6	0% helix, 17% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Interfaces

2 interfaces between chains.

A–B · 495 Å² buried · 6 hydrogen bonds · protein-protein
A–P · 484 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (engineered, methylation).

Compared structures

2YYR · Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3… · the same entry in another collection · chain A against A, TM-score 1.00
Q9D0P5 · AlphaFold monomer V2.0 prediction for pygopus homolog 1 (Q9D0P5) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9D0P5
Elsewhere: RCSB PDB 2YYR · PDBe 2YYR · UniProt Q9D0P5

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