SMTL ID : 5kh6.1

SETDB1 in complex with a fragment candidate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: Q.84, V.85, W.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.85 EDO.3: 6 residues within 4Å: Chain A: K.18, K.19, R.20, K.22, L.53, H.57 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.18, A:K.22, A:K.22 Water bridges: A:K.18, A:S.51 EDO.14: 7 residues within 4Å: Chain A: G.55, N.56, R.126, P.127, L.128 Ligands: SO4.8, CL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.55, A:N.56 EDO.19: 5 residues within 4Å: Chain A: S.114, Y.115, D.182, L.185, W.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.114, A:Y.115, A:D.182

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 6 residues within 4Å: Chain A: D.110, G.111, Y.112, E.197, R.205 Ligands: 6SU.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.205 Salt bridges: A:E.197 pi-Cation interactions: A:Y.112

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

SO4.4: 2 residues within 4Å: Chain A: H.25, K.26 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.26 Water bridges: A:H.25, A:K.26 Salt bridges: A:H.25 SO4.5: 4 residues within 4Å: Chain A: D.81, G.82, N.83, Q.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.81, A:N.83, A:Q.84 SO4.6: 3 residues within 4Å: Chain A: T.117, Q.118, S.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.117, A:Q.118, A:S.119, A:S.119 SO4.7: 1 residues within 4Å: Chain A: R.14 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.14 SO4.8: 5 residues within 4Å: Chain A: P.127, L.128, K.129 Ligands: CL.10, EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.128

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 1 residues within 4Å: Chain A: R.20 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: L.128, K.129 Ligands: SO4.8, EDO.14 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: L.53, S.54, H.57 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: G.36 Ligand excluded by PLIP

1 x 6SU: methyl 3-(methylsulfonylamino)benzoate(Non-covalent)

6SU.13: 10 residues within 4Å: Chain A: F.107, D.110, G.111, A.113, S.139, C.140, F.143, Y.200, S.203 Ligands: DMS.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.143 Hydrogen bonds: A:G.111 Water bridges: A:G.111, A:Y.200, A:S.203

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.15: 7 residues within 4Å: Chain A: Y.79, K.80, F.108, Y.112, A.113, S.114, W.198 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.80, A:A.113, A:S.114 Water bridges: A:E.197, A:W.198 PEG.16: 9 residues within 4Å: Chain A: E.94, N.97, K.99, N.100, Y.115, Y.151, R.154, G.183, S.184 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.115, A:R.154, A:S.184 Water bridges: A:R.201 PEG.17: 3 residues within 4Å: Chain A: K.101, R.103, D.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.101, A:R.103, A:D.182

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.18: 4 residues within 4Å: Chain A: E.1, N.2, Q.33, T.34 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.33 Hydrogen bonds: A:N.2

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 5 residues within 4Å: Chain A: K.19, T.21, T.23, H.25, W.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walker, J.R. et al., SETDB1 in complex with a fragment candidate. To be published

Release Date

2016-09-21

Peptides

Histone-lysine N-methyltransferase SETDB1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SETDB1