SMTL ID : 8eqi.2 (1 other biounit)

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.2.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x U2M- TYR- DGL- DSN- SER- DAS- ARG- VAL: Cyclopeptide des4.2.0(Non-covalent)

U2M-TYR-DGL-DSN-SER-DAS-ARG-VAL.1: 18 residues within 4Å: Chain A: H.29, P.30, N.96, S.97, H.139, H.140, G.148, F.149, D.178, H.180, A.207, F.209, N.211, D.271, L.278, G.309, Y.311 Ligands: ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.30, A:F.149, A:F.149, A:F.209, A:F.209, A:L.278 Hydrogen bonds: A:N.96, A:S.97, A:S.97, A:N.211 Water bridges: A:S.97

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: U2M-TYR-DGL-DSN-SER-DAS-ARG-VAL.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271

2 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.176, A:D.178, A:H.180, A:S.199 K.4: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.189, A:D.192, A:V.195, A:Y.228, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watson, P.R. et al., Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6. Acs Chem.Biol. (2023)

Release Date

2023-04-19

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Hdac6 protein

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