SMTL ID : 3b3b.1

Crystal structure of E. coli Aminopeptidase N in complex with tryptophan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.318, H.322, E.341, Y.402 Ligands: TRP.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.318, A:H.322, A:E.341, A:E.341, TRP.4

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

NA.2: 4 residues within 4Å: Chain A: S.353, D.354, G.356, R.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.353, A:R.358 NA.3: 1 residues within 4Å: Chain A: D.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.473, A:D.473, A:D.473

1 x TRP: TRYPTOPHAN(Non-covalent)

TRP.4: 18 residues within 4Å: Chain A: Q.140, E.142, A.143, F.279, M.281, A.283, M.284, E.285, H.318, E.319, H.322, K.340, E.341, N.394, Y.397, Y.402, Q.842 Ligands: ZN.1 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:Q.140, A:M.281 Hydrogen bonds: A:Q.140, A:E.285, A:E.319, A:K.340, A:Y.402 Water bridges: A:M.281, A:A.283 Salt bridges: A:H.318, A:H.322, A:K.340 pi-Stacking: A:Y.397

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.5: 5 residues within 4Å: Chain A: M.281, G.282, Y.296, R.804, R.846 6 PLIP interactions: 6 interactions with chain A Water bridges: A:Y.296, A:R.314 Salt bridges: A:K.295, A:R.804, A:R.804, A:R.846

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: A.552, L.553, W.567, S.584, D.587, A.588, S.591 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.553, A:D.587, A:S.591, A:S.591 Water bridges: A:L.553, A:L.554, A:F.557, A:S.584 GOL.7: 3 residues within 4Å: Chain A: R.690, V.691, E.692 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.691, A:E.692, A:E.692 GOL.8: 8 residues within 4Å: Chain A: Y.681, R.702, Q.724, E.727, A.728, N.729, N.730, D.733 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.681, A:R.702, A:R.702, A:N.729, A:N.729, A:D.733 Water bridges: A:Q.724, A:E.727, A:N.729

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Addlagatta, A. et al., Structural basis for the unusual specificity of Escherichia coli aminopeptidase N. Biochemistry (2008)

Release Date

2008-05-06

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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