SMTL ID : 5g10.1

Pseudomonas aeruginosa HDAH bound to 9,9,9 trifluoro-8,8-dihydroy-N-phenylnonanamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 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: Y.191, R.194, V.197, S.199, F.226 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.191, A:R.194, A:V.197, A:F.226, H2O.8 K.6: 5 residues within 4Å: Chain B: Y.191, R.194, V.197, S.199, F.226 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.191, B:R.194, B:V.197, B:F.226, H2O.20 K.7: 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.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: Y.191, R.194, V.197, S.199, F.226 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Y.191, C:R.194, C:V.197, C:F.226, H2O.32 K.14: 5 residues within 4Å: Chain D: Y.191, R.194, V.197, S.199, F.226 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Y.191, D:R.194, D:V.197, D:F.226, H2O.44 K.15: 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

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

6DK.4: 19 residues within 4Å: Chain A: T.23, D.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: P.338, L.339, F.342 Ligands: ZN.1 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.152, A:F.152, A:F.152, A:F.208, A:F.208, B:L.339, B:F.342, B:F.342 Hydrogen bonds: A:Y.312 Water bridges: A:T.23 pi-Stacking: B:F.342 6DK.8: 19 residues within 4Å: Chain A: L.339, F.342 Chain B: T.23, L.24, D.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 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.24, B:F.152, B:F.152, B:F.152, B:F.208, B:F.208, B:F.208, B:F.208, A:L.339, A:F.342 Hydrogen bonds: B:T.23, B:T.23, B:Y.312 pi-Stacking: A:F.342 6DK.12: 19 residues within 4Å: Chain C: T.23, D.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: P.338, L.339, F.342 Ligands: ZN.9 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:L.339, D:F.342, D:F.342, C:F.152, C:F.152, C:F.152, C:F.208, C:F.208 pi-Stacking: D:F.342 Hydrogen bonds: C:T.23 Water bridges: C:T.23 6DK.16: 19 residues within 4Å: Chain C: L.339, F.342 Chain D: T.23, L.24, D.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 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.24, D:F.152, D:F.152, D:F.152, D:F.208, D:F.208, D:F.208, D:F.208, C:L.339, C:F.342 Hydrogen bonds: D:T.23, D:H.143, D:H.182, D:Y.312 pi-Stacking: C:F.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kramer, A. et al., Crystal Structure of a Histone Deacetylase Homologue from Pseudomonas aeruginosa. Biochemistry (2016)

Release Date

2016-11-30

Peptides

HDAH: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

HDAH

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