SMTL ID : 3q9e.3 (5 other biounits)

Crystal structure of H159A APAH complexed with acetylspermine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x SP5: N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide(Non-covalent)

SP5.1: 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.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.156, A:Y.168, A:F.225 Hydrogen bonds: A:G.167, B:E.106 SP5.5: 14 residues within 4Å: Chain A: Y.83 Chain B: Y.19, E.117, P.156, H.158, G.167, Y.168, C.169, H.197, F.225, D.284, P.290, Y.323 Ligands: ZN.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.19, B:P.156, B:Y.168, B:F.225 Hydrogen bonds: B:Y.19, B:E.117, B:E.117, B:G.167, B:H.197

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.193, D.195, H.197, S.216, L.217 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.193, A:D.195, A:H.197, 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.193, B:D.195, B:H.197, B:S.216

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

NA.3: 4 residues within 4Å: Chain A: F.206, R.209, V.212, T.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.206, A:R.209, A:T.243 Water bridges: A:T.244 NA.7: 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.4: 6 residues within 4Å: Chain A: D.195, H.197, D.284, G.321, Y.323 Ligands: SP5.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.195, A:D.195, A:H.197, A:D.284 ZN.8: 7 residues within 4Å: Chain B: H.158, D.195, H.197, D.284, G.321, Y.323 Ligands: SP5.5 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
C

B
K

Acetylpolyamine amidohydrolase

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