SMTL ID : 3q9f.1 (5 other biounits)

Crystal Structure of APAH complexed with CAPS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.1: 12 residues within 4Å: Chain A: E.117, H.158, H.159, G.167, Y.168, D.195, H.197, F.225, D.284, G.321, G.322 Ligands: ZN.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.117, A:F.225, A:F.225 Hydrogen bonds: A:Y.168, A:G.322 Salt bridges: A:H.158, A:H.159, A:H.197 CXS.7: 14 residues within 4Å: Chain B: E.117, P.156, H.158, H.159, G.167, Y.168, D.195, H.197, F.225, D.284, I.291, G.321, Y.323 Ligands: ZN.11 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:E.117, B:F.225, B:F.225, B:F.225, B:I.291 Hydrogen bonds: B:Y.168, B:D.195 Salt bridges: B:H.158, B:H.159, B:H.197

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: H.54, G.55, R.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.55 Water bridges: A:T.58 Salt bridges: A:H.54, A:R.180 PO4.8: 3 residues within 4Å: Chain B: H.54, G.55, R.180 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.55 Water bridges: B:G.55, B:E.57, B:R.180, B:R.180 Salt bridges: B:H.54, B:R.180

3 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: D.193, D.195, H.197, S.216, L.217, H.218 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.193, A:D.195, A:H.197, A:S.216, A:L.217 K.5: 5 residues within 4Å: Chain A: F.286, E.287, D.289, S.292, F.294 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.286, A:D.289, A:S.292, A:S.292, H2O.3 K.9: 6 residues within 4Å: Chain B: D.193, D.195, H.197, S.216, L.217, H.218 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.193, B:D.195, B:H.197, B:S.216, B:L.217

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: F.206, R.209, V.212, T.243, T.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.209, A:T.243 Water bridges: A:T.243 NA.10: 4 residues within 4Å: Chain B: F.206, R.209, V.212, T.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.209, B:T.243 Water bridges: B:T.243

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: D.195, H.197, D.284 Ligands: CXS.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.195, A:D.195, A:H.197, A:D.284 ZN.11: 5 residues within 4Å: Chain B: D.195, F.196, H.197, D.284 Ligands: CXS.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.195, B:D.195, B:H.197, B:D.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lombardi, P.M. et al., Structure of prokaryotic polyamine deacetylase reveals evolutionary functional relationships with eukaryotic histone deacetylases . Biochemistry (2011)

Release Date

2011-03-02

Peptides

Acetylpolyamine amidohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
I

Acetylpolyamine amidohydrolase

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