SMTL ID : 9c0o.1

Crystal structure of DmCfp1 PHD finger bound to H3K4me3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

hetero-1-1-mer

Ligands

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 3 residues within 4Å: Chain A: E.28, W.30 Chain B: R.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.2, B:R.2, A:E.28 Salt bridges: A:E.28

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: C.12, C.17, H.32 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.12, A:C.17, A:H.32 ZN.3: 4 residues within 4Å: Chain A: C.24, C.27, C.51, C.54 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.24, A:C.27, A:C.51, A:C.54 ZN.4: 2 residues within 4Å: Chain A: H.45, R.66 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.45, A:R.66

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

SO4.5: 2 residues within 4Å: Chain A: R.52, K.55 7 PLIP interactions: 7 interactions with chain A Water bridges: A:Q.4, A:Q.4, A:R.52, A:R.52, A:K.55 Salt bridges: A:R.52, A:K.55 SO4.6: 2 residues within 4Å: Chain A: T.39, E.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40 Water bridges: A:K.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gregoire, S. et al., Structural insights into an atypical histone binding mechanism by a PHD finger. Structure (2024)

Release Date

2024-07-03

Peptides

CXXC-type zinc finger protein 1: A
Histone H3.3C: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

CXXC-type zinc finger protein 1

Histone H3.3C