SMTL ID : 6in3.1

Crystal structure of DOT1L in complex with 18-Crown-6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x O4B: 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE(Non-covalent)

O4B.1: 4 residues within 4Å: Chain A: R.99, P.100, S.101, T.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.102

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

SAH.2: 23 residues within 4Å: Chain A: P.131, E.132, V.133, Y.134, G.135, E.136, T.137, D.159, G.161, S.162, G.163, Q.166, V.167, V.183, E.184, K.185, A.186, G.219, D.220, F.221, F.237, N.239, F.243 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.137, A:G.161, A:Q.166, A:K.185, A:D.220, A:F.221, A:N.239 Water bridges: A:E.132, A:Y.134, A:S.162 pi-Stacking: A:F.221

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

SO4.3: 3 residues within 4Å: Chain A: R.201, K.205, H.211 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.201, A:K.205, A:H.211 SO4.4: 4 residues within 4Å: Chain A: R.227, Q.250, E.253, R.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.250 Salt bridges: A:R.227, A:R.254 SO4.5: 6 residues within 4Å: Chain A: L.156, V.158, Y.181, R.229, N.232, T.233 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.229 SO4.6: 2 residues within 4Å: Chain A: H.249, K.252 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.284 Salt bridges: A:H.249, A:K.252 SO4.7: 3 residues within 4Å: Chain A: E.37, H.107, Q.110 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.106, A:Q.110 Salt bridges: A:H.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, T. et al., Crown Ethers as Transthyretin Amyloidogenesis Inhibitor. To Be Published

Release Date

2019-10-30

Peptides

Histone-lysine N-methyltransferase, H3 lysine-79 specific: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase, H3 lysine-79 specific