SMTL ID : 3b3c.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 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, PLU.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.117, A:E.152, A:E.152, A:H.256 ZN.2: 6 residues within 4Å: Chain A: H.97, D.117, E.151, D.179 Ligands: ZN.1, PLU.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.97, A:D.117, A:D.179, A:D.179

1 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: E.151, L.155, C.227, S.228 Ligands: PLU.11 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.151, A:C.227, H2O.3, H2O.3

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

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

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

NA.5: 3 residues within 4Å: Chain A: Q.6, A.8, T.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.6, A:A.8, A:T.9, A:T.9 NA.6: 3 residues within 4Å: Chain A: G.24, S.27, S.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.28 NA.7: 3 residues within 4Å: Chain A: T.38, Y.73, N.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.74, A:N.74 NA.8: 2 residues within 4Å: Chain A: Q.54, A.55 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.55 NA.9: 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.10: 4 residues within 4Å: Chain A: V.17, D.18, A.19, K.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.17, A:A.19 Water bridges: A:S.20

1 x PLU: LEUCINE PHOSPHONIC ACID(Non-covalent)

PLU.11: 15 residues within 4Å: Chain A: H.97, D.117, E.151, E.152, D.179, Y.225, C.227, M.242, F.244, F.248, Y.251, H.256 Ligands: ZN.1, ZN.2, K.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.244, A:F.244, A:F.248, A:Y.251 Hydrogen bonds: A:Y.251

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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