SMTL ID : 3b3s.1

Crystal structure of the M180A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 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, LEU.13 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.117, A:E.152, A:E.152, A:H.256, H2O.5 ZN.2: 7 residues within 4Å: Chain A: H.97, D.117, E.151, E.152, D.179 Ligands: ZN.1, LEU.13 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.97, A:D.117, A:E.151, A:D.179, H2O.5

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

NA.3: 3 residues within 4Å: Chain A: L.213, P.214, S.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.213, A:S.215 NA.4: 4 residues within 4Å: Chain A: V.17, D.18, A.19, K.273 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.17, A:A.19 Water bridges: A:K.273, A:K.273 NA.5: 3 residues within 4Å: Chain A: D.47, W.48, S.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.47, A:S.51 NA.6: 1 residues within 4Å: Chain A: Y.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.206 NA.7: 2 residues within 4Å: Chain A: T.194, T.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.194 Water bridges: A:S.199 NA.8: 1 residues within 4Å: Chain A: H.234 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.196 NA.9: 2 residues within 4Å: Chain A: Q.54, A.55 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.55 NA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

SCN.11: 4 residues within 4Å: Chain A: T.194, S.199, T.202, Q.203 No protein-ligand interaction detected (PLIP) SCN.12: 2 residues within 4Å: Chain A: Q.7, A.8 No protein-ligand interaction detected (PLIP)

1 x LEU: LEUCINE(Non-covalent)

LEU.13: 12 residues within 4Å: Chain A: E.151, E.152, D.179, Y.225, C.227, F.244, F.248, Y.251, I.255, H.256 Ligands: ZN.1, ZN.2 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.244, A:F.244, A:F.248, A:Y.251, A:I.255 Hydrogen bonds: A:Y.225, A:C.227, L.13, L.13 Salt bridges: 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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