SMTL ID : 5vi6.1

Crystal structure of histone deacetylase 8 in complex with trapoxin A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

monomer

Ligands

1 x PHE- PHE- CPI- 5OM: Trapoxin A(Non-covalent)

PHE-PHE-CPI-5OM.1: 21 residues within 4Å: Chain A: K.28, Y.95, D.96, W.136, H.137, H.138, G.146, F.147, C.148, D.173, H.175, F.203, Q.258, D.262, M.269, G.298, G.299, Y.301 Ligands: ZN.2, EDO.8, EDO.10 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.95, A:F.147, A:F.147, A:F.147, A:F.203, A:F.203, A:F.203 Hydrogen bonds: A:D.96, A:D.96, A:D.96, A:H.137, A:H.138, A:D.173, A:G.299, A:Y.301 pi-Stacking: A:Y.95

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 8 residues within 4Å: Chain A: H.137, D.173, L.174, H.175, D.262, G.299, Y.301 Ligands: PHE-PHE-CPI-5OM.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.173, A:H.175, A:D.262

2 x K: POTASSIUM ION(Non-covalent)

K.3: 9 residues within 4Å: Chain A: D.171, L.172, D.173, H.175, H.176, G.177, S.194, L.195, H.196 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.171, A:D.171, A:D.173, A:H.175, A:S.194 K.4: 6 residues within 4Å: Chain A: F.184, S.185, T.187, V.190, M.191, Y.220 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.187, A:V.190, A:Y.220, H2O.4, H2O.9

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

EDO.5: 6 residues within 4Å: Chain A: A.57, S.58, M.59, M.62, Q.75, F.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.59 Water bridges: A:A.57, A:E.60 EDO.6: 5 residues within 4Å: Chain A: R.161, R.162, K.163, F.164, E.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.161 EDO.7: 7 residues within 4Å: Chain A: S.16, E.18, Y.19, M.22, P.54, V.56, A.109 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.18, A:P.54, A:A.109 EDO.8: 6 residues within 4Å: Chain A: K.28, F.147, P.268, M.269, Y.301 Ligands: PHE-PHE-CPI-5OM.1 No protein-ligand interaction detected (PLIP) EDO.9: 8 residues within 4Å: Chain A: P.276, V.277, R.308, C.309, Y.312, L.341, E.342, I.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.341 EDO.10: 6 residues within 4Å: Chain A: G.201, F.202, F.203, P.204, G.205 Ligands: PHE-PHE-CPI-5OM.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.201, A:G.201 Water bridges: A:G.201, A:F.203 EDO.11: 8 residues within 4Å: Chain A: H.138, A.139, K.140, S.145, D.178, G.179, F.203, P.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.138, A:K.140, A:S.145, A:D.178 EDO.12: 9 residues within 4Å: Chain A: L.26, Y.106, A.107, I.110, W.136, F.147, C.148, Y.149, L.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.106, A:F.147, A:L.150 EDO.13: 10 residues within 4Å: Chain A: C.23, D.24, L.26, I.29, R.32, A.33, V.36, S.133, W.136, W.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.23, A:R.32, A:R.32 Water bridges: A:A.33 EDO.14: 5 residues within 4Å: Chain A: V.209, R.356, Q.359, I.360, Y.363 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.356 Water bridges: A:R.356

2 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.15: 8 residues within 4Å: Chain A: M.191, Y.219, Y.220, A.249, F.250, N.367, L.368, K.369 No protein-ligand interaction detected (PLIP) DIO.16: 6 residues within 4Å: Chain A: T.64, F.65, V.154, L.158, A.183, F.184 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porter, N.J. et al., Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8. ACS Chem. Biol. (2017)

Release Date

2017-09-06

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 8