SMTL ID : 8uwp.2 (1 other biounit)

Crystal structure of SETDB1 Tudor domain in complex with MR46747

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

1 x XRU: (3S)-N-(4-chloro-3-{[2-(diethylamino)ethyl]carbamoyl}phenyl)-3-(diethylamino)pyrrolidine-1-carboxamide(Non-covalent)

XRU.1: 13 residues within 4Å: Chain A: Y.90, W.97, Y.99, F.119, D.121, Y.123, W.180, W.185, F.201, D.204, R.206, E.208 Ligands: SO4.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.90, A:Y.99, A:Y.99, A:F.119, A:W.185, A:F.201, A:F.201 Hydrogen bonds: A:E.208 Water bridges: A:Y.90, A:Y.90 Salt bridges: A:D.121, A:D.204 pi-Cation interactions: A:W.97, A:W.97

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

SO4.2: 2 residues within 4Å: Chain A: H.36, K.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.37, A:N.58 Salt bridges: A:H.36 SO4.3: 3 residues within 4Å: Chain A: N.94, R.206 Ligands: XRU.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.92, A:N.94 Salt bridges: A:R.206 SO4.4: 6 residues within 4Å: Chain A: K.29, K.30, R.31, L.64, H.68 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.30 Water bridges: A:K.33, A:K.33 Salt bridges: A:H.68 SO4.5: 6 residues within 4Å: Chain A: K.51, L.63, L.64, S.65, H.68 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.65 Salt bridges: A:K.51, A:H.68

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: F.118, G.122, Y.123, A.124, F.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.123 EDO.7: 6 residues within 4Å: Chain A: Y.90, K.91, D.92, A.124, S.125, W.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.90 Water bridges: A:Y.90, A:K.91 EDO.8: 2 residues within 4Å: Chain A: S.84, T.142 No protein-ligand interaction detected (PLIP)

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

UNX.9: 3 residues within 4Å: Chain A: R.31, S.62, L.63 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shrestha, S. et al., Crystal structure of SETDB1 Tudor domain in complex with MR46747. To be published

Release Date

2023-11-22

Peptides

Histone-lysine N-methyltransferase SETDB1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone-lysine N-methyltransferase SETDB1

Related Entries With Identical Sequence