SMTL ID : 5g17.1

Bordetella Alcaligenes HDAH (T101A) bound to 9,9,9-trifluoro-8,8- dihydroxy-N-phenylnonanamide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.180, H.182, D.268 Ligands: 6DK.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: 6DK.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: 4 residues within 4Å: Chain C: D.180, H.182, D.268 Ligands: 6DK.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: 4 residues within 4Å: Chain D: D.180, H.182, D.268 Ligands: 6DK.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.178, A:H.182, A:S.201, A:L.202 K.3: 5 residues within 4Å: Chain A: W.191, D.194, V.197, T.199, Y.226 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.194, A:V.197, A:Y.226, H2O.12, H2O.12 K.6: 5 residues within 4Å: Chain B: D.178, D.180, H.182, S.201, L.202 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.178, B:D.178, B:H.182, B:S.201, B:L.202 K.7: 5 residues within 4Å: Chain B: W.191, D.194, V.197, T.199, Y.226 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.194, B:V.197, B:Y.226, H2O.29, H2O.30 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.178, C:H.182, C:S.201, C:L.202 K.11: 5 residues within 4Å: Chain C: W.191, D.194, V.197, T.199, Y.226 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.194, C:V.197, C:Y.226, H2O.47, H2O.47 K.14: 5 residues within 4Å: Chain D: D.178, D.180, H.182, S.201, L.202 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.178, D:D.178, D:H.182, D:S.201, D:L.202 K.15: 5 residues within 4Å: Chain D: W.191, D.194, V.197, T.199, Y.226 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.194, D:V.197, D:Y.226, H2O.65, H2O.65

4 x 6DK: 9,9,9-tris(fluoranyl)-8,8-bis(oxidanyl)-~{N}-phenyl-nonanamide(Non-covalent)

6DK.4: 17 residues within 4Å: Chain A: 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 C: E.340, F.341 Ligands: ZN.1 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:I.100, A:F.152, A:F.152, A:F.208, A:F.208, C:E.340, C:F.341, C:F.341 Hydrogen bonds: A:Y.312 Water bridges: C:F.341 6DK.8: 17 residues within 4Å: Chain B: 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: E.340, F.341 Ligands: ZN.5 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:F.152, B:F.152, B:F.208, B:F.208, B:F.208, D:E.340, D:F.341, D:F.341 Water bridges: D:F.341 6DK.12: 17 residues within 4Å: Chain A: E.340, F.341 Chain C: 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.9 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:E.340, A:F.341, A:F.341, C:I.100, C:F.152, C:F.152, C:F.208, C:F.208 Water bridges: A:F.341 Hydrogen bonds: C:Y.312 6DK.16: 17 residues within 4Å: Chain B: E.340, F.341 Chain D: 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 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:E.340, B:F.341, B:F.341, D:F.152, D:F.152, D:F.208, D:F.208, D:F.208 Water bridges: B:F.341 Hydrogen bonds: D:H.143, D:Y.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyners, C. et al., The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket. Biochim. Biophys. Acta (2017)

Release Date

2017-04-12

Peptides

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE