SMTL ID : 3q9c.1 (5 other biounits)

Crystal Structure of H159A APAH complexed with N8-acetylspermidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x Q9C: N-{4-[(3-aminopropyl)amino]butyl}acetamide(Non-covalent)

Q9C.1: 16 residues within 4Å: Chain A: Y.19, E.117, P.156, H.158, G.167, Y.168, C.169, D.195, H.197, F.225, D.284, G.321, Y.323 Chain B: Y.83, E.106 Ligands: ZN.3 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.156, A:Y.168, A:F.225 Hydrogen bonds: A:E.117, A:E.117, A:G.167, B:Y.83, B:E.106 Water bridges: A:E.17 Q9C.5: 16 residues within 4Å: Chain A: Y.83, E.106 Chain B: Y.19, E.117, P.156, H.158, G.167, Y.168, C.169, D.195, H.197, F.225, D.284, G.321, Y.323 Ligands: ZN.7 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.156, B:Y.168, B:F.225 Hydrogen bonds: B:G.167, B:Y.168, A:Y.83, A:E.106 Water bridges: A:T.90

2 x K: POTASSIUM ION(Non-covalent)

K.2: 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.6: 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 ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.195, H.197, D.284, G.321, Y.323 Ligands: Q9C.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.195, A:D.195, A:H.197, A:D.284, Q9C.1 ZN.7: 5 residues within 4Å: Chain B: D.195, H.197, D.284, G.321 Ligands: Q9C.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.195, B:D.195, B:H.197, B:D.284, Q9C.5

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

NA.4: 4 residues within 4Å: Chain A: F.206, R.209, V.212, T.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.209, A:R.209 Water bridges: A:T.243 NA.8: 4 residues within 4Å: Chain B: F.206, R.209, V.212, T.243 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.243 Water bridges: B:T.243

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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