SMTL ID : 5g11.1

Pseudomonas aeruginosa HDAH bound to PFSAHA.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-tetramer

Ligands

4 x 7H1: 2,2,3,3,4,4,5,5,6,6,7,7-dodecakis(fluoranyl)-~{N}-oxidanyl-~{N}'-phenyl-octanediamide(Non-covalent)

7H1.1: 16 residues within 4Å: Chain A: T.23, L.24, D.100, H.142, H.143, G.151, F.152, D.180, H.182, F.208, D.268, L.275 Chain B: P.338, L.339, F.342 Ligands: ZN.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.24, B:L.339, B:F.342 Hydrogen bonds: A:G.310 Water bridges: A:G.311, A:G.311 7H1.5: 16 residues within 4Å: Chain A: P.338, L.339, F.342 Chain B: T.23, D.100, H.142, H.143, G.151, F.152, D.180, H.182, F.208, D.268, L.275, G.310 Ligands: ZN.6 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.339, A:F.342 Hydrogen bonds: B:T.23, B:H.143 Water bridges: B:G.311, B:G.311, B:G.311 Halogen bonds: B:G.151 7H1.9: 16 residues within 4Å: Chain C: T.23, L.24, D.100, H.142, H.143, G.151, F.152, D.180, H.182, F.208, D.268, L.275 Chain D: P.338, L.339, F.342 Ligands: ZN.10 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.339, D:F.342, C:L.24 Hydrogen bonds: C:T.23, C:G.310 Water bridges: C:G.311, C:G.311 7H1.13: 16 residues within 4Å: Chain C: P.338, L.339, F.342 Chain D: T.23, D.100, H.142, H.143, G.151, F.152, D.180, H.182, F.208, D.268, L.275, G.310 Ligands: ZN.14 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:L.339, C:F.342 Hydrogen bonds: D:H.143 Water bridges: D:G.311, D:G.311, D:G.311 Halogen bonds: D:G.151

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.142, D.180, H.182, D.268 Ligands: 7H1.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.180, A:D.180, A:H.182, A:D.268, 7H1.1 ZN.6: 4 residues within 4Å: Chain B: D.180, H.182, D.268 Ligands: 7H1.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.180, B:D.180, B:H.182, B:D.268, 7H1.5 ZN.10: 5 residues within 4Å: Chain C: H.142, D.180, H.182, D.268 Ligands: 7H1.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.180, C:D.180, C:H.182, C:D.268, 7H1.9 ZN.14: 4 residues within 4Å: Chain D: D.180, H.182, D.268 Ligands: 7H1.13 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.180, D:D.180, D:H.182, D:D.268, 7H1.13

8 x K: POTASSIUM ION(Non-covalent)

K.3: 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.4: 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.3 K.7: 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.9 K.8: 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.11: 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.12: 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.14 K.15: 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.19 K.16: 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

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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