SMTL ID : 3kqi.2 (1 other biounit)

crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-2-2-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.28, C.31, C.55, C.58 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.28, A:C.31, A:C.55, A:C.58 ZN.2: 4 residues within 4Å: Chain A: C.13, C.15, H.36, C.39 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.13, A:C.15, A:H.36, A:C.39 ZN.7: 4 residues within 4Å: Chain C: C.28, C.31, C.55, C.58 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.28, C:C.31, C:C.55, C:C.58 ZN.8: 4 residues within 4Å: Chain C: C.13, C.15, H.36, C.39 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.13, C:C.15, C:H.36, C:C.39

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: A.30, C.31, C.58, T.61, H.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.30, A:T.61 Water bridges: A:H.62 GOL.9: 5 residues within 4Å: Chain C: A.30, C.31, C.58, T.61, H.62 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.30, C:T.61, C:T.61 Water bridges: C:H.62

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: K.68, K.69, K.70 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain C: K.68, K.69, K.70 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: K.68, R.71, T.72 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: R.23, S.38 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: K.68, R.71, T.72 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain C: R.23, S.38 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wen, H. et al., Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation. J.Biol.Chem. (2010)

Release Date

2010-02-02

Peptides

PHD finger protein 2: AC
H3K4Me3 peptide: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

PHD finger protein 2

H3K4Me3 peptide

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