SMTL ID : 4q4e.1

Crystal structure of E.coli aminopeptidase N in complex with actinonin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.318, H.322, E.341 Ligands: BB2.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.318, A:H.322, A:E.341, A:E.341

1 x BB2: ACTINONIN(Non-covalent)

BB2.2: 17 residues within 4Å: Chain A: N.280, M.281, G.282, A.283, E.285, Y.296, H.318, E.319, H.322, E.341, D.348, Y.397, Y.402, R.804, R.846 Ligands: ZN.1, GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.318 Hydrogen bonds: A:G.282 Water bridges: A:K.340, A:K.340

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Y.296, D.311, R.314, V.315 Ligands: BB2.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.311 GOL.4: 6 residues within 4Å: Chain A: N.644, G.812, R.846, E.849, P.850, R.853 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.644, A:R.846 Water bridges: A:R.853 GOL.5: 6 residues within 4Å: Chain A: T.414, L.415, L.416, G.417, N.528, V.530 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.416, A:N.528 Water bridges: A:N.420, A:N.420, A:N.528, A:V.530, A:V.530 GOL.6: 5 residues within 4Å: Chain A: T.414, A.507, V.530, C.555, E.556 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.414, A:S.529, A:E.556, A:N.581 GOL.7: 7 residues within 4Å: Chain A: S.133, A.136, F.215, D.237, A.275, V.276, D.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.277, A:D.277 Water bridges: A:D.237 GOL.8: 6 residues within 4Å: Chain A: K.562, E.648, L.649, F.650, D.651, R.856 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.648, A:L.649, A:D.651 Water bridges: A:K.562 GOL.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.10: 6 residues within 4Å: Chain A: F.725, A.734, E.755, Y.756, K.759, W.760 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.755, A:K.759 Water bridges: A:H.726

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

NA.11: 5 residues within 4Å: Chain A: T.47, D.49, V.56, V.57, T.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.47, A:D.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ganji, R.J. et al., Structural basis for the inhibition of M1 family aminopeptidases by the natural product actinonin: Crystal structure in complex with E. coli aminopeptidase N. Protein Sci. (2015)

Release Date

2015-04-15

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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