SMTL ID : 6bhd.1

Crystal structure of SETDB1 with a modified H3 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

hetero-1-1-mer

Ligands

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

UNX.1: 6 residues within 4Å: Chain A: Y.106, A.107, F.126, D.127, D.128 Ligands: UNX.24 Ligand excluded by PLIP UNX.2: 2 residues within 4Å: Chain A: L.146, K.147 Ligand excluded by PLIP UNX.3: 2 residues within 4Å: Chain A: P.170, N.171 Ligand excluded by PLIP UNX.4: 4 residues within 4Å: Chain A: K.37, F.63, N.65, K.66 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: N.115, K.117 Ligand excluded by PLIP UNX.6: 5 residues within 4Å: Chain A: Y.165, A.168, Y.169, N.171, R.172 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: Y.59, R.144 Ligands: UNX.20 Ligand excluded by PLIP UNX.8: 1 residues within 4Å: Chain A: K.119 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: V.89, T.113, Y.169 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: E.112, N.115, Y.169, R.172 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: E.198, V.199 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: V.199, D.200, G.201 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: G.201, S.202, R.219 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: I.183, K.184 Ligands: UNX.15 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: L.182 Ligands: UNX.14 Ligand excluded by PLIP UNX.16: 1 residues within 4Å: Chain A: T.149 Ligand excluded by PLIP UNX.17: 3 residues within 4Å: Chain A: N.74, H.75, D.152 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: G.129, C.158 Chain B: K.12 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain A: T.52, K.57 Ligand excluded by PLIP UNX.20: 5 residues within 4Å: Chain A: K.57, Y.59, S.72, G.73 Ligands: UNX.7 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: K.40, D.127 Ligand excluded by PLIP UNX.22: 2 residues within 4Å: Chain A: L.176, Q.181 Ligand excluded by PLIP UNX.23: 3 residues within 4Å: Chain A: R.172, P.173, M.174 Ligand excluded by PLIP UNX.24: 4 residues within 4Å: Chain A: Y.106, F.126, D.128 Ligands: UNX.1 Ligand excluded by PLIP UNX.25: 5 residues within 4Å: Chain A: W.192, K.193, F.208, L.209, D.210 Ligand excluded by PLIP UNX.26: 2 residues within 4Å: Chain A: L.182, R.195 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain A: K.37, R.38 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain A: I.183, K.184, E.225 Ligand excluded by PLIP UNX.29: 3 residues within 4Å: Chain A: I.142, C.143, P.145 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain A: S.179, G.180, Q.181 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain A: P.170, R.172 Ligand excluded by PLIP UNX.32: 3 residues within 4Å: Chain A: L.146, K.147, T.149 Ligand excluded by PLIP UNX.33: 1 residues within 4Å: Chain A: K.212 Ligand excluded by PLIP UNX.34: 1 residues within 4Å: Chain A: F.228 Ligand excluded by PLIP UNX.36: 2 residues within 4Å: Chain B: S.8, T.9 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.35: 1 residues within 4Å: Chain A: T.167 No protein-ligand interaction detected (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

2017-12-06

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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