SMTL ID : 4a69.1 (1 other biounit)

Structure of HDAC3 bound to corepressor and inositol tetraphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.170, H.172, D.259 Ligands: ACT.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.170, A:D.170, A:H.172, A:D.259, ACT.2

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

ACT.2: 10 residues within 4Å: Chain A: H.134, H.135, G.143, C.145, D.170, H.172, D.259, G.296, Y.298 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.298 Salt bridges: A:H.134, A:H.135, A:H.172

2 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: D.168, D.170, H.172, S.191, F.192 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.168, A:D.168, A:D.170, A:H.172, A:S.191 K.4: 4 residues within 4Å: Chain A: F.181, T.184, V.187, Y.217 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.181, A:T.184, A:V.187, H2O.4, H2O.4

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Y.51, L.112, Q.113, T.116 No protein-ligand interaction detected (PLIP) GOL.6: 5 residues within 4Å: Chain A: T.116, N.119, N.120, E.156, Y.160 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.116, A:T.116, A:N.119, A:N.120, A:Y.160, A:Y.160

1 x I0P: D-MYO INOSITOL 1,4,5,6 TETRAKISPHOSPHATE(Non-covalent)

I0P.7: 14 residues within 4Å: Chain A: H.17, A.20, G.21, H.22, K.25, R.265, V.300, R.301, Y.331 Chain B: K.63, Y.84, Y.85, K.88, K.89 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:G.21, A:R.265, A:R.301, B:Y.84, B:Y.85 Water bridges: A:V.300, B:K.89 Salt bridges: A:H.17, A:K.25, A:K.25, A:R.265, B:K.63, B:K.63, B:K.88, B:K.88, B:K.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watson, P.J. et al., Structure of Hdac3 Bound to Co-Repressor and Inositol Tetraphosphate. Nature (2012)

Release Date

2012-01-11

Peptides

HISTONE DEACETYLASE 3,: A
NUCLEAR RECEPTOR COREPRESSOR 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

HISTONE DEACETYLASE 3,

NUCLEAR RECEPTOR COREPRESSOR 2

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