SMTL ID : 6j6t.1

Crystal Structure of HDA15 HD domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.168, H.170, D.259 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.168, A:D.168, A:H.170, A:D.259 ZN.5: 3 residues within 4Å: Chain B: D.168, H.170, D.259 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.168, B:D.168, B:H.170, B:D.259 ZN.10: 4 residues within 4Å: Chain C: H.131, D.168, H.170, D.259 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.168, C:D.168, C:H.170, C:D.259 ZN.13: 3 residues within 4Å: Chain D: D.168, H.170, D.259 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.168, D:D.168, D:H.170, D:D.259

4 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.166, D.168, H.170, S.189, L.190, H.191 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.166, A:D.166, A:D.168, A:H.170, A:L.190 K.6: 6 residues within 4Å: Chain B: D.166, D.168, H.170, S.189, L.190, H.191 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.166, B:D.166, B:H.170, B:S.189, B:L.190 K.11: 6 residues within 4Å: Chain C: D.166, D.168, H.170, S.189, L.190, H.191 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.166, C:D.166, C:H.170, C:S.189, C:L.190 K.14: 6 residues within 4Å: Chain D: D.166, D.168, H.170, S.189, L.190, H.191 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.166, D:D.166, D:D.168, D:H.170, D:S.189

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

SO4.3: 3 residues within 4Å: Chain A: T.59, K.60, Q.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.60 SO4.4: 3 residues within 4Å: Chain A: T.68, S.69, E.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.69, A:E.70 SO4.7: 4 residues within 4Å: Chain B: Q.181, N.182, K.183, S.184 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.183, B:S.184 SO4.8: 2 residues within 4Å: Chain B: N.300, R.302 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.300 SO4.9: 3 residues within 4Å: Chain B: T.59, K.60, R.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.60 Water bridges: B:Q.61 Salt bridges: B:R.101 SO4.12: 2 residues within 4Å: Chain C: P.30, R.34 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:E.94, C:S.17 Salt bridges: C:R.34 SO4.15: 3 residues within 4Å: Chain D: P.30, D.31, R.34 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.34 Salt bridges: D:R.34 SO4.16: 3 residues within 4Å: Chain D: I.58, T.59, K.60 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, C.Y. et al., Structure of Arabidopsis HISTONE DEACETYLASE15. Plant Physiol. (2020)

Release Date

2020-01-22

Peptides

Histone deacetylase 15: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Histone deacetylase 15