SMTL ID : 4qeo.1

crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 16 residues within 4Å: Chain A: K.365, G.366, W.367, E.401, Y.402, R.457, F.458, I.459, N.460, H.461, Y.502, A.520, C.521, Y.522, C.523 Chain D: K.9 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.402 Hydrogen bonds: A:K.365, A:W.367, A:W.367, A:E.401, A:Y.402, A:N.460, A:H.461, A:H.461, A:Y.522 Water bridges: A:R.361

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.292, C.306, C.334, C.338 Ligands: ZN.3, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.292, A:C.306, A:C.334, A:C.338 ZN.3: 5 residues within 4Å: Chain A: C.298, C.334, C.340, C.344 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.298, A:C.334, A:C.340, A:C.344 ZN.4: 5 residues within 4Å: Chain A: C.292, C.294, C.298, C.304 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.292, A:C.294, A:C.298, A:C.304 ZN.5: 4 residues within 4Å: Chain A: C.463, C.521, C.523, C.528 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.463, A:C.521, A:C.523, A:C.528

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, J. et al., Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE. Mol.Cell (2014)

Release Date

2014-07-30

Peptides

Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4: A
Histone H3: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
P

Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4

Histone H3

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