SMTL ID : 5jjy.1

Crystal structure of SETD2 bound to histone H3.3 K36M peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.67, C.69, C.84, C.88 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.69, A:C.84, A:C.88 ZN.2: 5 residues within 4Å: Chain A: C.84, C.97, C.101, C.107 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.84, A:C.97, A:C.101, A:C.107 ZN.3: 5 residues within 4Å: Chain A: C.199, C.246, C.248, C.253, R.254 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.199, A:C.246, A:C.248, A:C.253

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

SAH.4: 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 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.130, A:W.130, A:I.170, A:Y.172, A:Y.173, A:N.196, A:H.197, A:H.197, A:F.247 Salt bridges: A:H.171

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

SCN.5: 8 residues within 4Å: Chain A: M.65, Q.66, C.67, N.90, C.97, S.98, C.101, P.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.90, A:S.98 SCN.6: 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.7: 2 residues within 4Å: Chain A: C.31, K.36 No protein-ligand interaction detected (PLIP) SCN.8: 3 residues within 4Å: Chain A: C.107, S.108, Q.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.116 SCN.9: 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

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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