SMTL ID : 3b3v.1

Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 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, VAL.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, VAL.8 ZN.2: 5 residues within 4Å: Chain A: H.97, D.117, D.179 Ligands: ZN.1, VAL.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.97, A:D.117, A:D.179, A:D.179, VAL.8

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

NA.3: 2 residues within 4Å: Chain A: T.257, T.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.258 Water bridges: A:T.257, A:T.258 NA.4: 2 residues within 4Å: Chain A: Q.54, A.55 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.55 NA.5: 3 residues within 4Å: Chain A: T.38, Y.73, N.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.38, A:N.74

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 No protein-ligand interaction detected (PLIP)

1 x VAL: VALINE(Non-covalent)

VAL.8: 13 residues within 4Å: Chain A: H.97, D.117, E.151, E.152, D.179, M.180, C.227, A.228, F.244, I.255, H.256 Ligands: ZN.1, ZN.2 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:F.244, A:I.255 Hydrogen bonds: A:E.151 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

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