SMTL ID : 9cux.1

Crystal Structure of SETDB1 Tudor domain in complex with UNC100016

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

1 x 01: (2E)-N-(4-{[6-(dimethylamino)hexyl]amino}-2-{[5-(dimethylamino)pentyl]amino}quinazolin-6-yl)but-2-enamide

01.1: 18 residues within 4Å: Chain A: Y.90, D.92, Y.99, F.119, D.121, Y.123, W.180, W.185, R.198, F.201, D.204, K.205, R.206, C.207, E.208 Ligands: EDO.6, EDO.7, UNX.13 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.90, A:Y.123, A:Y.123, A:F.201, A:R.206, A:E.208 Hydrogen bonds: A:Y.90, A:D.92, A:D.92, A:C.207, A:C.207 Water bridges: A:D.204 Salt bridges: A:D.121, A:D.204 pi-Cation interactions: A:Y.90, A:W.180

2 x SO4: SULFATE ION

SO4.2: 4 residues within 4Å: Chain A: K.37, H.74, K.89, Y.133 9 PLIP interactions: 9 interactions with chain A Water bridges: A:K.37, A:K.37, A:K.37, A:K.37, A:Y.133, A:Y.133 Salt bridges: A:K.37, A:H.74, A:K.89 SO4.3: 2 residues within 4Å: Chain A: H.36, K.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.37 Water bridges: A:H.36 Salt bridges: A:H.36

9 x EDO: 1,2-ETHANEDIOL

EDO.4: 3 residues within 4Å: Chain A: F.16, Q.17, G.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.18 Water bridges: A:Q.17, A:Q.17, A:Q.17 EDO.5: 6 residues within 4Å: Chain A: F.118, G.122, A.124, F.154, Y.211, S.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.214 Water bridges: A:S.214, A:T.215 EDO.6: 5 residues within 4Å: Chain A: R.198, C.207, W.209 Ligands: 01.1, EDO.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.198 EDO.7: 6 residues within 4Å: Chain A: Y.90, Y.123, E.208, W.209 Ligands: 01.1, EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.209 EDO.8: 6 residues within 4Å: Chain A: K.29, K.30, R.31, K.33, L.64, H.68 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.29, A:K.33, A:K.33 Water bridges: A:K.29, A:S.62 EDO.9: 4 residues within 4Å: Chain A: K.51, L.64, S.65, H.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.65, A:H.68 Water bridges: A:S.65, A:S.65 EDO.10: 2 residues within 4Å: Chain A: L.139, K.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.140 Water bridges: A:E.144 EDO.11: 7 residues within 4Å: Chain A: L.80, S.84, R.85, V.86, P.134, I.135, P.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.85, A:I.135 Water bridges: A:C.136 EDO.12: 1 residues within 4Å: Chain A: E.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.156 Water bridges: A:E.144, A:D.153

4 x UNX: UNKNOWN ATOM OR ION

UNX.13: 3 residues within 4Å: Chain A: Y.99, D.121 Ligands: 01.1 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain A: E.157, A.161 No protein-ligand interaction detected (PLIP) UNX.15: 3 residues within 4Å: Chain A: T.128, Q.129, S.130 No protein-ligand interaction detected (PLIP) UNX.16: 2 residues within 4Å: Chain A: V.22, S.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lastname, F.M., Crystal Structure of SETDB1 Tudor domain in complex with UNC100016. To be published

Release Date

2024-10-02

Peptides

Histone-lysine N-methyltransferase SETDB1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SETDB1

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