SMTL ID : 4zun.1

Crystal structure of acetylpolyamine amidohydrolase from Mycoplana ramosa in complex with a thiol inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x SS9: 5-[(3-aminopropyl)amino]pentane-1-thiol(Non-covalent)

SS9.1: 16 residues within 4Å: Chain A: Y.19, H.158, H.159, G.167, Y.168, D.195, H.197, F.225, D.284, I.291, G.321, Y.323 Chain B: Y.83, E.106 Ligands: ZN.4, ZN.5 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.168, A:F.225, A:I.291, A:Y.323 Water bridges: A:E.17, A:Y.168, A:Y.168 Hydrogen bonds: B:Y.83, B:E.106 SS9.11: 16 residues within 4Å: Chain A: Y.83, E.106 Chain B: Y.19, H.158, H.159, G.167, Y.168, D.195, H.197, F.225, D.284, I.291, G.321, Y.323 Ligands: ZN.9, ZN.10 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:E.106 Hydrophobic interactions: B:Y.168, B:F.225, B:I.291, B:Y.323 Water bridges: B:Y.168, B:Y.168

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.7: 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.3: 4 residues within 4Å: Chain A: F.206, R.209, V.212, T.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.212 Water bridges: A:T.244 NA.8: 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:T.243, B:T.243 Water bridges: B:T.243

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: D.195, H.197, D.284 Ligands: SS9.1, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.195, A:D.195, A:H.197, A:D.284 ZN.5: 5 residues within 4Å: Chain A: H.158, H.159, D.195 Ligands: SS9.1, ZN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.158, A:H.159, H2O.12 ZN.9: 5 residues within 4Å: Chain B: D.195, H.197, D.284 Ligands: ZN.10, SS9.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.195, B:D.195, B:H.197, B:D.284 ZN.10: 5 residues within 4Å: Chain B: H.158, H.159, D.195 Ligands: ZN.9, SS9.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.158, B:H.159, H2O.28

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: K.15, W.75, K.84, G.85, E.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.15, A:K.84 Water bridges: A:E.86 GOL.12: 5 residues within 4Å: Chain B: K.15, W.75, K.84, G.85, E.86 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.15, B:K.84 GOL.13: 6 residues within 4Å: Chain A: L.229, E.234 Chain B: R.96, T.97, S.98, P.99 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:E.233, B:S.98 Hydrogen bonds: B:R.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Decroos, C. et al., Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase. Biochemistry (2015)

Release Date

2015-07-29

Peptides

Acetylpolyamine aminohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetylpolyamine aminohydrolase

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