SMTL ID : 7vyw.1

Crystal structure of the chromodomain of Arabidopsis LHP1 in complex with methylated histone H3K9 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x PCA- THR- ALA- ARG- M3L- SER: methylated histone H3K9 peptide(Non-covalent)

PCA-THR-ALA-ARG-M3L-SER.1: 15 residues within 4Å: Chain A: G.1, G.2, F.3, Y.4, E.5, I.6, W.25, R.26, W.28, A.32, E.36, P.37, E.39, N.40, S.43 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.3, A:Y.4, A:Y.4, A:I.6, A:W.25, A:N.40 Hydrogen bonds: A:G.1, A:G.2, A:Y.4, A:Y.4, A:I.6, A:R.26, A:E.36, A:N.40, A:N.40, A:N.40, A:S.43, A:S.43 Water bridges: A:E.36 pi-Cation interactions: A:Y.4, A:W.25, A:W.28, A:W.28

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: V.14, R.15, K.16, G.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.16, A:G.17 Water bridges: A:V.14 SO4.3: 2 residues within 4Å: Chain A: R.15, K.16 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.13, A:K.16, A:K.16 Salt bridges: A:R.15, A:K.16 SO4.4: 3 residues within 4Å: Chain A: K.24, P.29, E.30 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.30 Water bridges: A:K.24, A:E.30, A:E.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain. J.Biol.Chem. (2022)

Release Date

2022-02-02

Peptides

Chromo domain-containing protein LHP1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Chromo domain-containing protein LHP1

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