SMTL ID : 5yq1.1

Crystal structure of E.coli aminopeptidase N in complex with O-Methyl-L-tyrosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 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: 0A1.2 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, 0A1.2

1 x 0A1: O-methyl-L-tyrosine(Non-covalent)

0A1.2: 15 residues within 4Å: Chain A: Q.140, E.142, M.281, A.283, M.284, E.285, H.318, E.319, H.322, K.340, E.341, Y.397, Y.402, Q.842 Ligands: ZN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:M.281, A:Y.397 Hydrogen bonds: A:A.283, A:K.340, A:E.341 Water bridges: A:N.280, A:A.283, A:Q.842 Salt bridges: A:H.318, A:H.322

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

MLI.3: 6 residues within 4Å: Chain A: R.662, E.663, T.666, R.707, F.711, A.743 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.711 Water bridges: A:E.663, A:T.666 Salt bridges: A:R.662, A:R.662, A:R.707 MLI.4: 6 residues within 4Å: Chain A: F.725, A.734, E.755, Y.756, K.759, W.760 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.725, A:Y.756 Salt bridges: A:K.759, A:K.759 MLI.5: 2 residues within 4Å: Chain A: K.472, K.566 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.566 Salt bridges: A:K.472

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: Y.397, Y.402, R.846 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.403 GOL.7: 5 residues within 4Å: Chain A: S.722, H.726, C.748, A.751, E.755 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.722, A:S.722, A:E.755 GOL.8: 9 residues within 4Å: Chain A: N.600, R.603, H.604, Q.608, P.609, L.610, E.660, V.661, A.664 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.600, A:Q.608 Water bridges: A:L.610, A:E.660, A:A.664 GOL.9: 8 residues within 4Å: Chain A: A.552, L.553, W.567, L.572, L.575, D.587, A.588, S.591 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.553, A:L.553, A:S.591, A:S.591, A:S.591 GOL.10: 2 residues within 4Å: Chain A: R.182, Q.185 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.182, A:R.182, A:R.182 GOL.11: 2 residues within 4Å: Chain A: R.690, E.692 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marapaka, A.K. et al., Crystal structure of E.coli aminopeptidase N in complex with O-Methyl-L-tyrosine. To Be Published

Release Date

2018-11-07

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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