SMTL ID : 6j9j.1

crystal structure of SESTD2 in complex with H3.3S31phK36M peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.53, C.55, C.70, C.74 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.53, A:C.55, A:C.70, A:C.74 ZN.2: 5 residues within 4Å: Chain A: C.70, C.83, C.87, C.93 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.70, A:C.83, A:C.87, A:C.93 ZN.3: 4 residues within 4Å: Chain A: C.185, C.232, C.234, C.239 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.185, A:C.232, A:C.234, A:C.239

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

SAH.4: 19 residues within 4Å: Chain A: K.114, G.115, W.116, I.156, H.157, Y.158, Y.159, R.179, F.180, M.181, N.182, H.183, Y.220, Q.230, K.231, C.232, F.233, C.234, L.243 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:W.116, A:W.116, A:W.116, A:H.157, A:Y.158, A:Y.159, A:H.183, A:H.183, A:Q.230, A:Q.230, A:F.233 Salt bridges: A:H.157

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

SCN.5: 6 residues within 4Å: Chain A: M.80, T.191, K.193 Chain B: P.10, H.11, R.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.193 Water bridges: B:R.12 SCN.6: 5 residues within 4Å: Chain A: T.111, E.112, K.113, K.114, F.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.113 SCN.7: 6 residues within 4Å: Chain A: H.183, Q.221, F.222, R.240, G.244, G.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.240 SCN.8: 5 residues within 4Å: Chain A: S.2, C.3, D.7, C.17, K.22 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Armache, A. et al., Histone H3.3 phosphorylation amplifies stimulation-induced transcription. Nature (2020)

Release Date

2020-02-26

Peptides

Histone-lysine N-methyltransferase SETD2: A
H3.3S31phK36M(29-42): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase SETD2

H3.3S31phK36M(29-42)

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