SMTL ID : 2gh6.5 (4 other biounits)

Crystal structure of a HDAC-like protein with 9,9,9-trifluoro-8-oxo-N-phenylnonan amide bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.142, D.180, H.182, D.268 Ligands: CF3.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.180, A:D.180, A:H.182, A:D.268 ZN.5: 4 residues within 4Å: Chain B: D.180, H.182, D.268 Ligands: CF3.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.180, B:D.180, B:H.182, B:D.268 ZN.9: 5 residues within 4Å: Chain C: H.142, D.180, H.182, D.268 Ligands: CF3.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.180, C:D.180, C:H.182, C:D.268 ZN.13: 5 residues within 4Å: Chain D: H.142, D.180, H.182, D.268 Ligands: CF3.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.180, D:D.180, D:H.182, D:D.268

8 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.178, D.180, H.182, S.201, L.202 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.178, A:D.180, A:H.182, A:S.201, A:L.202 K.3: 4 residues within 4Å: Chain A: W.191, D.194, V.197, Y.226 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:W.191, A:D.194, A:V.197, H2O.1, H2O.5 K.6: 6 residues within 4Å: Chain B: D.178, D.180, H.182, S.201, L.202, H.203 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.178, B:D.180, B:H.182, B:S.201, B:L.202 K.7: 4 residues within 4Å: Chain B: W.191, D.194, V.197, Y.226 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:W.191, B:D.194, B:V.197, H2O.12 K.10: 5 residues within 4Å: Chain C: D.178, D.180, H.182, S.201, L.202 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.178, C:D.180, C:H.182, C:S.201, C:L.202 K.11: 4 residues within 4Å: Chain C: W.191, D.194, V.197, Y.226 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:W.191, C:D.194, C:V.197, H2O.20, H2O.20 K.14: 6 residues within 4Å: Chain D: D.178, D.180, H.182, S.201, L.202, H.203 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.178, D:D.180, D:H.182, D:S.201, D:L.202 K.15: 4 residues within 4Å: Chain D: W.191, D.194, V.197, Y.226 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:W.191, D:D.194, D:V.197, H2O.28

4 x CF3: 9,9,9-TRIFLUORO-8-OXO-N-PHENYLNONANAMIDE(Non-covalent)

CF3.4: 17 residues within 4Å: Chain A: L.21, I.100, P.140, H.142, H.143, G.151, F.152, C.153, D.180, H.182, F.208, D.268, E.309, G.310, Y.312 Chain B: F.341 Ligands: ZN.1 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.21, A:I.100, A:F.152, A:F.152, A:F.208, A:F.208, A:F.208, B:F.341, B:F.341, B:F.341 CF3.8: 17 residues within 4Å: Chain A: F.341 Chain B: L.21, I.100, P.140, H.142, H.143, G.151, F.152, C.153, D.180, H.182, F.208, D.268, E.309, G.310, Y.312 Ligands: ZN.5 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.21, B:I.100, B:F.152, B:F.208, B:F.208, B:F.208, A:F.341, A:F.341 CF3.12: 17 residues within 4Å: Chain C: L.21, I.100, P.140, H.142, H.143, G.151, F.152, C.153, D.180, H.182, F.208, D.268, E.309, G.310, Y.312 Chain D: F.341 Ligands: ZN.9 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.21, C:L.21, C:I.100, C:F.152, C:F.152, C:F.208, C:F.208, C:F.208, C:F.208, D:F.341, D:F.341, D:F.341 Hydrogen bonds: C:Y.312 Halogen bonds: C:D.180 CF3.16: 17 residues within 4Å: Chain C: F.341 Chain D: L.21, I.100, P.140, H.142, H.143, G.151, F.152, C.153, D.180, H.182, F.208, D.268, E.309, G.310, Y.312 Ligands: ZN.13 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.21, D:L.21, D:I.100, D:F.152, D:F.152, D:F.208, D:F.208, D:F.208, C:F.341, C:F.341, C:F.341 Hydrogen bonds: D:H.182, D:Y.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nielsen, T.K. et al., Complex structure of a bacterial class 2 histone deacetylase homologue with a trifluoromethylketone inhibitor. Acta Crystallogr.,Sect.F (2007)

Release Date

2007-03-20

Peptides

Histone deacetylase-like amidohydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Histone deacetylase-like amidohydrolase

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