SMTL ID : 6bhh.1

Crystal structure of SETDB1 with a modified H3 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-mer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: N.115, V.116, K.117 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.116, A:K.117 Water bridges: A:N.115 Salt bridges: A:K.117 SO4.2: 3 residues within 4Å: Chain A: H.43, K.44 Ligands: UNX.26 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.44 Water bridges: A:H.43, A:H.43, A:H.43, A:K.44, A:N.65 Salt bridges: A:H.43

26 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 6 residues within 4Å: Chain A: Y.165, A.168, Y.169, N.171, R.172 Ligands: UNX.12 Ligand excluded by PLIP UNX.4: 5 residues within 4Å: Chain A: K.57, Y.59, S.72, G.73 Ligands: UNX.6 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: D.24, R.144 Ligand excluded by PLIP UNX.6: 4 residues within 4Å: Chain A: D.24, Y.59, R.144 Ligands: UNX.4 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: K.44, D.79, H.81, Y.140 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain A: E.112, T.113, N.115 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: E.188 Chain B: G.10 Ligands: UNX.14 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: M.230, K.231 Ligands: UNX.11 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: M.230 Ligands: UNX.10 Ligand excluded by PLIP UNX.12: 4 residues within 4Å: Chain A: A.168, N.171, R.172 Ligands: UNX.3 Ligand excluded by PLIP UNX.13: 2 residues within 4Å: Chain A: K.178, S.179 Ligand excluded by PLIP UNX.14: 7 residues within 4Å: Chain A: E.186, E.188, R.223 Chain B: G.10, A.13, R.15 Ligands: UNX.9 Ligand excluded by PLIP UNX.15: 1 residues within 4Å: Chain A: D.211 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain A: G.201, S.202, R.219 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: K.147 Ligands: UNX.23 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: L.146, K.147 Ligands: UNX.23 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain A: K.58, L.70 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain A: E.164, K.231 Ligand excluded by PLIP UNX.21: 4 residues within 4Å: Chain A: D.128, G.129, C.158 Chain B: G.11 Ligand excluded by PLIP UNX.22: 1 residues within 4Å: Chain A: R.219 Ligand excluded by PLIP UNX.23: 2 residues within 4Å: Ligands: UNX.17, UNX.18 Ligand excluded by PLIP UNX.24: 4 residues within 4Å: Chain A: F.126, D.127, C.158, I.162 Ligand excluded by PLIP UNX.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.26: 3 residues within 4Å: Chain A: H.43, N.65 Ligands: SO4.2 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain A: G.180, R.195 Ligand excluded by PLIP UNX.28: 1 residues within 4Å: Chain B: K.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jurkowska, R.Z. et al., H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1. Nat Commun (2017)

Release Date

2017-11-22

Peptides

Histone-lysine N-methyltransferase SETDB1: A
Histone H3.1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase SETDB1

Histone H3.1

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