SMTL ID : 5icn.1

HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GLY- ALA- 6A0- ARG- HIS: GLY-ALA-6A0-ARG-HIS(Non-covalent)

GLY-ALA-6A0-ARG-HIS.1: 18 residues within 4Å: Chain B: Q.26, G.27, H.28, P.29, E.98, D.99, P.101, H.140, H.141, G.149, F.150, D.176, H.178, F.205, D.264, G.301, Y.303 Ligands: ZN.3 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:D.99, B:F.150, B:F.150, B:F.150 Hydrogen bonds: B:H.28, B:E.98, B:D.99, B:D.99, B:D.99, B:H.141, B:D.176, B:H.178, B:G.301, B:Y.303 pi-Stacking: B:H.28 GLY-ALA-6A0-ARG-HIS.6: 18 residues within 4Å: Chain D: Q.26, G.27, H.28, P.29, E.98, D.99, P.101, H.140, H.141, G.149, F.150, D.176, H.178, F.205, D.264, G.301, Y.303 Ligands: ZN.8 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:D.99, D:F.150, D:F.150, D:F.150 Hydrogen bonds: D:D.99, D:D.99, D:D.99, D:D.99, D:H.141, D:D.176, D:G.301 pi-Stacking: D:H.28

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 8 residues within 4Å: Chain A: K.146, Y.168, Y.169, K.172 Chain B: G.27, K.31, R.270, I.305 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Y.168, A:Y.168, A:Y.169, A:Y.177, B:G.27 Salt bridges: A:K.146, A:K.146, A:K.146, A:K.172, A:K.172, A:K.172, B:K.31, B:K.31, B:K.31, B:R.270, B:R.270 IHP.7: 8 residues within 4Å: Chain C: K.146, Y.168, Y.169, K.172 Chain D: G.27, K.31, R.270, I.305 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:Y.168, D:G.27 Salt bridges: C:K.146, C:K.146, C:K.146, C:K.172, C:K.172, C:K.172, D:K.31, D:K.31, D:K.31, D:R.270, D:R.270

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain B: D.176, I.177, H.178, D.264 Ligands: GLY-ALA-6A0-ARG-HIS.1 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.176, B:D.176, B:H.178, B:D.264 ZN.8: 5 residues within 4Å: Chain D: D.176, I.177, H.178, D.264 Ligands: GLY-ALA-6A0-ARG-HIS.6 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.176, D:D.176, D:H.178, D:D.264

4 x K: POTASSIUM ION(Non-covalent)

K.4: 7 residues within 4Å: Chain B: D.174, I.175, D.176, H.178, S.197, F.198, H.199 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.174, B:D.176, B:S.197 K.5: 5 residues within 4Å: Chain B: F.187, T.190, V.193, G.219, Y.222 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:F.187 K.9: 7 residues within 4Å: Chain D: D.174, I.175, D.176, H.178, S.197, F.198, H.199 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.174, D:D.176, D:S.197 K.10: 5 residues within 4Å: Chain D: F.187, T.190, V.193, G.219, Y.222 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:F.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watson, P.J. et al., Insights into the activation mechanism of class I HDAC complexes by inositol phosphates. Nat Commun (2016)

Release Date

2016-05-11

Peptides

Metastasis-associated protein MTA1: AC
Histone deacetylase 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Metastasis-associated protein MTA1

Histone deacetylase 1