SMTL ID : 3b3t.1

Crystal structure of the D118N mutant of the aminopeptidase from Vibrio proteolyticus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.117, E.152, H.256 Ligands: ZN.2, ILE.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.117, A:E.152, A:E.152, A:H.256, ILE.8 ZN.2: 5 residues within 4Å: Chain A: H.97, D.117, D.179 Ligands: ZN.1, ILE.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.97, A:D.117, A:D.179, A:D.179

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

NA.3: 1 residues within 4Å: Chain A: N.74 No protein-ligand interaction detected (PLIP) NA.4: 2 residues within 4Å: Chain A: Q.54, A.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.54 NA.5: 2 residues within 4Å: Chain A: T.257, T.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.258 Water bridges: A:Q.259

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

SCN.6: 4 residues within 4Å: Chain A: T.194, S.199, T.202, Q.203 No protein-ligand interaction detected (PLIP) SCN.7: 2 residues within 4Å: Chain A: Q.7, A.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.8 Water bridges: A:Q.7

1 x ILE: ISOLEUCINE(Non-covalent)

ILE.8: 14 residues within 4Å: Chain A: H.97, D.117, E.151, E.152, D.179, M.180, Y.225, C.227, F.248, Y.251, I.255, H.256 Ligands: ZN.1, ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.248, A:Y.251, A:I.255 Salt bridges: A:H.97, A:H.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ataie, N.J. et al., Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus. Biochemistry (2008)

Release Date

2007-11-27

Peptides

Bacterial leucyl aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bacterial leucyl aminopeptidase