SMTL ID : 5yq2.1

Crystal structure of E.coli aminopeptidase N in complex with Puromycin aminonucleoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 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: MLI.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.318, A:H.322, A:E.341, A:E.341, H2O.2

1 x GMC: (2R,3R,4S,5S)-4-AMINO-2-[6-(DIMETHYLAMINO)-9H-PURIN-9-YL]-5-(HYDROXYMETHYL)TETRAHYDRO-3-FURANOL(Non-covalent)

GMC.2: 7 residues within 4Å: Chain A: Y.397, L.399, Y.402, E.403, R.846, E.849 Ligands: MLI.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.403, A:R.846 Water bridges: A:R.314, A:L.399, A:Y.402, A:E.403 pi-Cation interactions: A:R.846

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: S.455, H.456, R.459 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.455, A:R.459, A:R.459 GOL.4: 7 residues within 4Å: Chain A: A.552, L.553, W.567, S.584, D.587, A.588, S.591 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.553, A:S.591, A:S.591 Water bridges: A:L.554, A:F.557, A:S.584

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

MLI.5: 8 residues within 4Å: Chain A: G.282, A.283, R.314, H.318, E.319, Y.402 Ligands: ZN.1, GMC.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.319 Water bridges: A:G.282, A:Y.296, A:R.314, A:R.314 Salt bridges: A:R.314, A:H.318 MLI.6: 7 residues within 4Å: Chain A: F.725, H.726, A.728, A.734, Y.756, K.759, W.760 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.726 Salt bridges: A:K.759, A:K.759

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 Puromycin aminonucleoside. 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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