SMTL ID : 3ewf.1 (4 other biounits)

Crystal Structure Analysis of human HDAC8 H143A variant complexed with substrate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x ACE- ARG- HIS- ALY- ALY: PEPTIDIC SUBSTRATE(Non-covalent)

ACE-ARG-HIS-ALY-ALY.1: 28 residues within 4Å: Chain A: Y.100, D.101, W.141, H.142, E.148, G.151, F.152, D.178, H.180, G.206, F.207, F.208, P.209, G.210, D.267, M.274, G.304, Y.306 Chain B: P.273, N.307, L.308, A.309, P.342 Chain C: F.191, G.220, K.221 Ligands: ZN.5, MCM.19 18 PLIP interactions: 12 interactions with chain A, 2 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: A:W.141, A:F.152, A:F.152, A:F.208, A:F.208, C:K.221, B:P.273, B:A.309 Hydrogen bonds: A:D.101, A:G.151, A:H.180, A:G.206, A:Y.306, C:K.221, B:L.308, B:A.309 Water bridges: A:F.208 Salt bridges: A:E.148 ACE-ARG-HIS-ALY-ALY.2: 28 residues within 4Å: Chain A: P.273, N.307, L.308, A.309, A.339, G.341, P.342 Chain B: I.94, E.95, G.97, Y.100, D.101, W.141, H.142, E.148, G.151, F.152, D.178, H.180, F.208, P.209, G.210, D.267, M.274, G.304, Y.306 Ligands: ZN.9, MCM.20 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.100, B:W.141, B:F.152, B:F.152, B:F.208, B:F.208, B:F.208, B:F.208, A:A.309 Hydrogen bonds: B:I.94, B:I.94, B:G.97, B:D.101, B:D.101, B:G.151, B:H.180, B:Y.306, A:A.309 Water bridges: B:F.208, B:F.208 Salt bridges: B:E.148 ACE-ARG-HIS-ALY-ALY.3: 29 residues within 4Å: Chain A: F.191, G.220, K.221 Chain C: Y.100, D.101, W.141, H.142, E.148, G.151, F.152, D.178, H.180, G.206, F.208, P.209, G.210, D.267, M.274, G.304, Y.306 Chain D: P.273, Y.306, N.307, L.308, A.309, A.339, P.342 Ligands: ZN.12, MCM.21 18 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: C:Y.100, C:W.141, C:F.152, C:F.152, C:F.208, C:F.208, C:F.208, D:A.309, A:F.191, A:K.221 Hydrogen bonds: C:D.101, C:G.151, C:G.206, C:Y.306, D:A.309, A:K.221 Water bridges: C:P.209 Salt bridges: C:E.148 ACE-ARG-HIS-ALY-ALY.4: 23 residues within 4Å: Chain C: P.273, N.307, L.308, A.309 Chain D: I.94, Y.100, D.101, W.141, H.142, E.148, G.151, F.152, D.178, H.180, F.208, P.209, G.210, D.267, M.274, G.304, Y.306 Ligands: ZN.16, MCM.22 20 PLIP interactions: 16 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.100, D:W.141, D:F.152, D:F.152, D:F.208, D:F.208, D:F.208, C:P.273, C:A.309 Hydrogen bonds: D:I.94, D:I.94, D:D.101, D:G.151, D:H.180, D:Y.306, C:L.308, C:A.309 Water bridges: D:F.208, D:F.208 Salt bridges: D:E.148

6 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: D.178, H.180, D.267 Ligands: ACE-ARG-HIS-ALY-ALY.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.267 ZN.8: 2 residues within 4Å: Chain A: H.375 Chain D: C.352 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:C.352, A:H.375, H2O.2 ZN.9: 4 residues within 4Å: Chain B: D.178, H.180, D.267 Ligands: ACE-ARG-HIS-ALY-ALY.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.178, B:D.178, B:H.180, B:D.267 ZN.12: 4 residues within 4Å: Chain C: D.178, H.180, D.267 Ligands: ACE-ARG-HIS-ALY-ALY.3 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.178, C:D.178, C:H.180, C:D.267 ZN.15: 2 residues within 4Å: Chain B: C.352 Chain C: H.375 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.375, B:C.352, H2O.5, H2O.9 ZN.16: 4 residues within 4Å: Chain D: D.178, H.180, D.267 Ligands: ACE-ARG-HIS-ALY-ALY.4 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.178, D:D.178, D:H.180, D:D.267

8 x K: POTASSIUM ION(Non-covalent)

K.6: 7 residues within 4Å: Chain A: D.176, L.177, 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.7: 5 residues within 4Å: Chain A: F.189, T.192, V.195, Y.225, S.226 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.189, A:T.192, A:V.195, A:Y.225, H2O.1 K.10: 7 residues within 4Å: Chain B: D.176, L.177, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.176, B:D.176, B:D.178, B:H.180, B:S.199 K.11: 4 residues within 4Å: Chain B: F.189, T.192, V.195, Y.225 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.189, B:T.192, B:V.195, B:Y.225, H2O.4 K.13: 7 residues within 4Å: Chain C: D.176, L.177, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.176, C:D.176, C:D.178, C:H.180, C:L.200 K.14: 5 residues within 4Å: Chain C: F.189, T.192, V.195, Y.225, S.226 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:F.189, C:T.192, C:Y.225, H2O.7, H2O.7 K.17: 7 residues within 4Å: Chain D: D.176, L.177, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.176, D:D.176, D:D.178, D:H.180, D:S.199 K.18: 5 residues within 4Å: Chain D: F.189, T.192, V.195, Y.225, S.226 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:F.189, D:T.192, D:V.195, D:Y.225, H2O.9

4 x MCM: 7-AMINO-4-METHYL-CHROMEN-2-ONE(Non-covalent)

MCM.19: 11 residues within 4Å: Chain A: K.33, Y.100, D.101, F.152 Chain B: K.33, F.152, P.273, M.274 Ligands: ACE-ARG-HIS-ALY-ALY.1, ACE-ARG-HIS-ALY-ALY.1, MCM.20 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:K.33, B:F.152, B:P.273, A:Y.100, A:F.152 Hydrogen bonds: A:D.101 Salt bridges: A:K.33 MCM.20: 12 residues within 4Å: Chain A: K.33, F.152, P.273, M.274, Y.306 Chain B: K.33, Y.100, D.101, F.152 Ligands: ACE-ARG-HIS-ALY-ALY.2, ACE-ARG-HIS-ALY-ALY.2, MCM.19 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:K.33, A:F.152, A:P.273, A:Y.306, B:Y.100, B:F.152 Hydrogen bonds: B:D.101 Salt bridges: B:K.33 MCM.21: 12 residues within 4Å: Chain C: K.33, Y.100, D.101, F.152 Chain D: K.33, F.152, P.273, M.274, Y.306 Ligands: ACE-ARG-HIS-ALY-ALY.3, ACE-ARG-HIS-ALY-ALY.3, MCM.22 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:Y.100, C:F.152, D:K.33, D:F.152, D:P.273, D:P.273, D:Y.306 Hydrogen bonds: C:D.101 Salt bridges: C:K.33 MCM.22: 11 residues within 4Å: Chain C: K.33, F.152, P.273, M.274 Chain D: K.33, Y.100, D.101, F.152 Ligands: ACE-ARG-HIS-ALY-ALY.4, ACE-ARG-HIS-ALY-ALY.4, MCM.21 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.100, D:F.152, C:K.33, C:F.152, C:P.273 Hydrogen bonds: D:D.101 Salt bridges: D:K.33

Links

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Citation

Dowling, D.P. et al., Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry (2008)

Release Date

2008-12-30

Peptides

Histone deacetylase 8: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Histone deacetylase 8

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