SMTL ID : 5jhn.1

Structure of G9a SET-domain with Histone H3K9Ala mutant peptide and bound S-adenosylmethionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

hetero-2-2-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.65, C.102, C.108, C.112 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.65, A:C.102, A:C.108, A:C.112 ZN.2: 7 residues within 4Å: Chain A: C.59, C.61, C.65, C.70, C.102 Ligands: ZN.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.59, A:C.61, A:C.65, A:C.70 ZN.3: 6 residues within 4Å: Chain A: C.59, C.72, C.102, C.106 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.59, A:C.72, A:C.102, A:C.106 ZN.4: 4 residues within 4Å: Chain A: C.200, C.253, C.255, C.260 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.200, A:C.253, A:C.255, A:C.260 ZN.6: 6 residues within 4Å: Chain C: C.59, C.72, C.102, C.106 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.59, C:C.72, C:C.102, C:C.106 ZN.7: 6 residues within 4Å: Chain C: C.65, C.102, C.108, C.112 Ligands: ZN.6, ZN.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.65, C:C.102, C:C.108, C:C.112 ZN.8: 6 residues within 4Å: Chain C: C.59, C.61, C.65, C.70 Ligands: ZN.6, ZN.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.59, C:C.61, C:C.65, C:C.70 ZN.9: 4 residues within 4Å: Chain C: C.200, C.253, C.255, C.260 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.200, C:C.253, C:C.255, C:C.260

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.5: 17 residues within 4Å: Chain A: M.133, G.134, W.135, S.169, Y.170, R.194, F.195, I.196, N.197, H.198, Y.239, F.243, K.247, F.251, T.252, C.253, Q.254 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.135, A:W.135, A:Y.170, A:N.197, A:N.197, A:H.198, A:H.198, A:Q.254 SAM.10: 16 residues within 4Å: Chain C: M.133, G.134, W.135, S.169, Y.170, R.194, F.195, I.196, N.197, H.198, Y.239, F.243, F.251, T.252, C.253, Q.254 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:W.135, C:W.135, C:S.169, C:N.197, C:N.197, C:H.198, C:H.198, C:Q.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jayaram, H. et al., S-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-07-06

Peptides

Histone-lysine N-methyltransferase EHMT2: AC
Histone H3.1 peptide with K9A mutation: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
F

D
G

Histone-lysine N-methyltransferase EHMT2

Histone H3.1 peptide with K9A mutation

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