SMTL ID : 5ikk.1

Structure of the histone deacetylase Clr3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.165, A.166, D.204, I.205, H.206, D.297, G.335 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.165, A:D.204, A:D.204, A:H.206, A:D.297 ZN.3: 3 residues within 4Å: Chain A: H.38, H.47, C.132 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.38, A:H.47, A:C.132 ZN.13: 7 residues within 4Å: Chain B: H.165, A.166, D.204, I.205, H.206, D.297, G.335 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.165, B:D.204, B:D.204, B:H.206, B:D.297 ZN.15: 3 residues within 4Å: Chain B: H.38, H.47, C.132 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.38, B:H.47, B:C.132

4 x K: POTASSIUM ION(Non-covalent)

K.2: 8 residues within 4Å: Chain A: F.215, Y.216, D.218, V.221, L.222, Y.223, R.254, T.255 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.218, A:V.221, A:R.254, H2O.1, H2O.3 K.4: 8 residues within 4Å: Chain A: D.202, D.204, H.206, H.207, G.208, S.225, L.226, H.227 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.202, A:D.202, A:D.204, A:H.206, A:S.225 K.14: 8 residues within 4Å: Chain B: F.215, Y.216, D.218, V.221, L.222, Y.223, R.254, T.255 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.218, B:V.221, B:R.254, H2O.10, H2O.11 K.16: 8 residues within 4Å: Chain B: D.202, D.204, H.206, H.207, G.208, S.225, L.226, H.227 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.202, B:D.202, B:D.204, B:H.206, B:S.225

6 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 4 residues within 4Å: Chain A: R.34, M.35, R.36, F.37 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.35, A:R.36, A:R.36 Water bridges: A:R.34 NO3.6: 7 residues within 4Å: Chain A: H.316, G.359, R.360, L.361 Chain B: Y.283, D.286, L.324 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.286, A:H.316, A:L.361 Water bridges: B:D.286, B:D.286, B:D.286, B:G.323, B:L.324, B:A.325 NO3.7: 7 residues within 4Å: Chain A: S.382, Q.383, Y.384, W.385, R.386, R.389, K.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.389, A:R.389 NO3.17: 4 residues within 4Å: Chain B: R.34, M.35, R.36, F.37 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.35, B:R.36, B:R.36 Water bridges: B:R.34 NO3.18: 7 residues within 4Å: Chain A: Y.283, D.286, L.324 Chain B: H.316, G.359, R.360, L.361 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:H.316, B:L.361 Water bridges: A:D.286, A:D.286, A:D.286, A:G.323, A:L.324, A:A.325 NO3.19: 7 residues within 4Å: Chain B: S.382, Q.383, Y.384, W.385, R.386, R.389, K.391 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.389, B:R.389

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

EDO.8: 9 residues within 4Å: Chain A: Y.272, T.364, Y.365, A.366, V.371 Chain B: R.386, C.387, R.389, E.470 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.364, A:A.366, B:R.386 EDO.9: 10 residues within 4Å: Chain A: R.410, Q.413, L.417, L.442, H.458, D.483, V.485, S.486, V.489, D.501 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.410, A:H.458, A:D.501 Water bridges: A:Q.413 EDO.10: 8 residues within 4Å: Chain A: D.50, R.52, R.53, G.336, Y.337, N.338, L.339, I.342 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.336 Water bridges: A:R.53, A:R.53 EDO.20: 9 residues within 4Å: Chain A: R.386, C.387, R.389, E.470 Chain B: Y.272, T.364, Y.365, A.366, V.371 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.364, B:A.366, A:R.386 EDO.21: 10 residues within 4Å: Chain B: R.410, Q.413, L.417, L.442, H.458, D.483, V.485, S.486, V.489, D.501 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.410, B:H.458, B:D.501 Water bridges: B:Q.413 EDO.22: 8 residues within 4Å: Chain B: D.50, R.52, R.53, G.336, Y.337, N.338, L.339, I.342 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.50, B:G.336 Water bridges: B:R.53, B:R.53

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

SO4.11: 5 residues within 4Å: Chain A: E.587, P.591, K.616, R.617, R.618 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.617, A:R.618 Salt bridges: A:K.616, A:R.617, A:R.618 SO4.23: 5 residues within 4Å: Chain B: E.587, P.591, K.616, R.617, R.618 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.617, B:R.618 Salt bridges: B:K.616, B:R.617, B:R.618

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 6 residues within 4Å: Chain A: P.397, K.398, D.399, A.400, V.402, D.403 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:P.397, A:D.399, A:V.402, H2O.5, H2O.6 MG.24: 6 residues within 4Å: Chain B: P.397, K.398, D.399, A.400, V.402, D.403 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:P.397, B:D.399, B:V.402, H2O.13, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Job, G. et al., SHREC Silences Heterochromatin via Distinct Remodeling and Deacetylation Modules. Mol.Cell (2016)

Release Date

2016-04-20

Peptides

Histone deacetylase clr3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histone deacetylase clr3