SMTL ID : 5jlb.1

Crystal structure of SETD2 bound to histone H3.3 K36I peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAH.1: 19 residues within 4Å: Chain A: K.128, G.129, W.130, I.170, H.171, Y.172, Y.173, R.193, F.194, M.195, N.196, H.197, Y.234, Q.244, K.245, C.246, F.247, C.248, L.257 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:W.130, A:W.130, A:I.170, A:Y.172, A:Y.172, A:Y.173, A:N.196, A:H.197, A:H.197, A:F.247 Water bridges: A:R.193 Salt bridges: A:H.171

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.2: 6 residues within 4Å: Chain A: H.197, Q.235, F.236, R.254, G.258, G.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.254, A:G.258 SCN.3: 4 residues within 4Å: Chain A: H.154, F.157, K.158, R.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.158 SCN.4: 6 residues within 4Å: Chain A: T.205, Q.206, K.207 Chain B: P.10, H.11, R.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.207

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: K.245, C.246, C.253, G.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.255 Water bridges: A:K.245, A:K.245, A:C.246 GOL.6: 6 residues within 4Å: Chain A: R.77, D.105, Y.106, C.107, S.108, Q.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.77, A:R.77, A:C.107, A:Q.116

3 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: C.67, C.69, C.84, C.88 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.69, A:C.84, A:C.88 ZN.8: 5 residues within 4Å: Chain A: C.84, C.97, C.101, C.107 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.84, A:C.97, A:C.101, A:C.107 ZN.9: 4 residues within 4Å: Chain A: C.199, C.246, C.248, C.253 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.199, A:C.246, A:C.248, A:C.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, S. et al., Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase. Genes Dev. (2016)

Release Date

2016-11-02

Peptides

Histone-lysine N-methyltransferase SETD2: A
Histone H3.3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase SETD2

Histone H3.3

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