SMTL ID : 4zup.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.195, H.197, D.284 Ligands: 5XA.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.195, A:D.195, A:H.197, A:D.284 ZN.2: 2 residues within 4Å: Chain A: H.146 Ligands: NO3.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.146 ZN.10: 4 residues within 4Å: Chain B: D.195, H.197, D.284 Ligands: 5XA.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.195, B:D.195, B:H.197, B:D.284 ZN.11: 2 residues within 4Å: Chain B: H.146 Ligands: NO3.17 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.146

4 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.4: 4 residues within 4Å: Chain A: F.206, R.209, V.212, T.243 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.206, A:R.209, A:V.212, A:T.243, H2O.5 K.12: 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 K.13: 4 residues within 4Å: Chain B: F.206, R.209, V.212, T.243 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.206, B:R.209, B:V.212, B:T.243, H2O.22

2 x 5XA: 5-amino-N-hydroxypentanamide(Non-covalent)

5XA.5: 11 residues within 4Å: Chain A: E.117, H.158, H.159, G.167, Y.168, D.195, H.197, F.225, D.284, Y.323 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.225, A:F.225 Hydrogen bonds: A:E.117, A:E.117, A:H.159, A:Y.168 Water bridges: A:E.17 5XA.14: 12 residues within 4Å: Chain B: E.117, H.158, H.159, G.167, Y.168, D.195, H.197, F.225, D.284, I.291, Y.323 Ligands: ZN.10 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.168, B:Y.168, B:F.225, B:I.291 Hydrogen bonds: B:E.117, B:H.159, B:Y.323 Water bridges: A:T.90

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: K.15, W.75, K.84, G.85, E.86, P.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.15, A:K.84 Water bridges: A:E.86 GOL.9: 4 residues within 4Å: Chain A: Y.231, A.232, E.233 Chain B: R.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.232, A:E.233 GOL.15: 6 residues within 4Å: Chain A: L.229, E.234 Chain B: R.96, T.97, S.98, P.99 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:E.233, A:E.234 Hydrogen bonds: B:R.96 GOL.18: 4 residues within 4Å: Chain B: L.266, T.307, A.310, S.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.307 Water bridges: B:L.266, B:A.270

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 3 residues within 4Å: Chain A: M.1, F.45, A.340 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.1 Water bridges: A:M.1, A:G.44, A:A.340 NO3.8: 4 residues within 4Å: Chain A: H.146, K.147, A.148 Ligands: ZN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.147, A:A.148 NO3.16: 3 residues within 4Å: Chain B: M.1, F.45, A.340 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.1 Water bridges: B:M.1, B:G.44, B:G.44 NO3.17: 4 residues within 4Å: Chain B: H.146, K.147, A.148 Ligands: ZN.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.147, B:A.148

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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