SMTL ID : 2yyr.1

Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

1 x ALA- ARG- THR- M3L- GLN- THR: H3K4Me3 peptide(Non-covalent)

ALA-ARG-THR-M3L-GLN-THR.1: 15 residues within 4Å: Chain A: Y.10, V.19, N.20, D.21, Q.23, A.25, I.26, L.27, E.29, W.35, Y.48, L.51, T.52, E.54, A.57 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.25, A:I.26, A:L.27, A:W.35, A:W.35, A:Y.48 Hydrogen bonds: A:A.25, A:L.27, A:E.29, A:Y.48, A:Y.48, A:A.57 Salt bridges: A:D.21 pi-Cation interactions: A:Y.10, A:W.35, A:W.35

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.12, C.15, H.37, C.40 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.12, A:C.15, A:H.37, A:C.40 ZN.3: 4 residues within 4Å: Chain A: C.28, C.32, C.61, C.64 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.28, A:C.32, A:C.61, A:C.64 ZN.4: 4 residues within 4Å: Chain B: C.12, C.15, H.37, C.40 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.12, B:C.15, B:H.37, B:C.40 ZN.5: 4 residues within 4Å: Chain B: C.28, C.32, C.61, C.64 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.28, B:C.32, B:C.61, B:C.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, Y. et al., Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide. To be Published

Release Date

2008-05-06

Peptides

Pygopus homolog 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pygopus homolog 1

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