SMTL ID : 3vh9.1

Crystal structure of Aeromonas proteolytica aminopeptidase complexed with 8-quinolinol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.117, E.152, H.256 Ligands: ZN.2, HQY.3, NA.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.117, A:E.152, A:E.152, A:H.256 ZN.2: 7 residues within 4Å: Chain A: H.97, D.117, E.151, E.152, D.179 Ligands: ZN.1, HQY.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.97, A:D.117, A:D.179, A:D.179

1 x HQY: quinolin-8-ol(Non-covalent)

HQY.3: 14 residues within 4Å: Chain A: H.97, D.117, E.151, E.152, D.179, Y.225, C.227, F.244, Y.251, I.255, H.256 Ligands: ZN.1, ZN.2, NA.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.244, A:Y.251, A:I.255

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

NA.4: 2 residues within 4Å: Chain A: T.194, T.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.197, A:T.197 Water bridges: A:T.197, A:S.199 NA.5: 2 residues within 4Å: Chain A: N.74 Ligands: NA.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.74 NA.6: 2 residues within 4Å: Chain A: T.206, Y.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.206, A:T.206, A:Y.218 NA.7: 1 residues within 4Å: Chain A: N.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.249, A:N.249 NA.8: 2 residues within 4Å: Chain A: T.268, S.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.268, A:S.270, A:S.270 NA.9: 1 residues within 4Å: Chain A: T.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.11, A:T.11 NA.10: 5 residues within 4Å: Chain A: E.151, E.152, H.256 Ligands: ZN.1, HQY.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.152 Water bridges: A:G.154 NA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.12: 2 residues within 4Å: Chain A: N.74 Ligands: NA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.74, A:N.74

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 3 residues within 4Å: Chain A: L.213, P.214, S.215 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: V.17, D.18, A.19, K.273 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: T.257, T.258 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: T.38, Y.73, N.74 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: S.71, G.72 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: Q.6, A.8, T.9 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: G.24, S.27, S.28 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: Y.183, K.184, D.266 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain A: G.219, F.220 Ligand excluded by PLIP

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.22: 4 residues within 4Å: Chain A: T.194, S.199, T.202, Q.203 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.202 SCN.23: 4 residues within 4Å: Chain A: A.12, W.13, Q.16, N.135 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 3 residues within 4Å: Chain A: S.28, S.31, F.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.28, A:S.31 Water bridges: A:T.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hanaya, K. et al., Potent inhibition of dinuclear zinc(II) peptidase, an aminopeptidase from Aeromonas proteolytica, by 8-quinolinol derivatives: inhibitor design based on Zn(2+) fluorophores, kinetic, and X-ray crystallographic study. J.Biol.Inorg.Chem. (2012)

Release Date

2012-05-02

Peptides

Bacterial leucyl aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bacterial leucyl aminopeptidase

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