SMTL ID : 4xo3.1

Crystal Structure of E. coli Aminopeptidase N in complex with L-Leucine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.293, H.297, E.316 Ligands: LEU.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.293, A:H.297, A:E.316, A:E.316, LEU.2

1 x LEU: LEUCINE(Non-covalent)

LEU.2: 15 residues within 4Å: Chain A: Q.115, E.117, M.256, A.258, M.259, E.260, H.293, E.294, H.297, K.315, E.316, Y.372, Y.377 Ligands: ZN.1, MLI.17 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:M.256, A:Y.372 Hydrogen bonds: A:E.260, A:Y.377 Water bridges: A:A.258 Salt bridges: A:H.293, A:H.297

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

NA.3: 4 residues within 4Å: Chain A: S.328, D.329, G.331, R.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.329, A:R.333 NA.4: 2 residues within 4Å: Chain A: D.448 Ligands: NA.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.448, A:D.448, A:D.448 NA.5: 2 residues within 4Å: Chain A: H.767, F.770 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.770, A:F.770 NA.6: 1 residues within 4Å: Chain A: A.98 6 PLIP interactions: 6 interactions with chain A Water bridges: A:A.98, A:T.100, A:T.100, A:T.100, A:T.100, A:T.100 NA.7: 1 residues within 4Å: Chain A: Y.540 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.540, A:Y.540 NA.8: 2 residues within 4Å: Chain A: E.119, E.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.367 Water bridges: A:E.367 NA.9: 3 residues within 4Å: Chain A: D.448, Y.540 Ligands: NA.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.448 Water bridges: A:D.448 NA.10: 3 residues within 4Å: Chain A: E.422, D.428, S.430 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.422, A:S.430 Water bridges: A:R.433 NA.11: 3 residues within 4Å: Chain A: Q.15, I.16, L.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.15, A:I.16, A:L.134 NA.12: 6 residues within 4Å: Chain A: Y.127, L.128, R.130, V.133, P.179, C.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.128, A:R.130, A:C.180 Water bridges: A:Y.181 NA.13: 1 residues within 4Å: Chain A: Q.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.160

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 8 residues within 4Å: Chain A: M.256, Y.372, T.373, L.374, Y.377, E.378, R.821 Ligands: MLI.17 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.378, A:E.378, A:R.821, A:R.821 Water bridges: A:G.257, L.2

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

MLI.15: 6 residues within 4Å: Chain A: R.637, E.638, T.641, R.682, F.686, A.718 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.686 Water bridges: A:R.637, A:E.638, A:E.638, A:T.641, A:T.641, A:R.682 Salt bridges: A:R.637, A:R.637, A:R.682 MLI.16: 7 residues within 4Å: Chain A: N.255, M.256, N.268, K.270, P.775, N.776, R.779 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.255, A:N.776 Water bridges: A:K.270, A:K.270, A:K.270, A:K.270 Salt bridges: A:K.270, A:R.779 MLI.17: 8 residues within 4Å: Chain A: G.257, V.290, H.293, E.294, D.323, Y.377 Ligands: LEU.2, GOL.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.290 Water bridges: A:G.257, A:A.258 Salt bridges: A:H.293, A:H.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Addlagatta, A. et al., Crystal Structure of E. coli Aminopeptidase N in complex with L-Leucine. To Be Published

Release Date

2016-01-27

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

Related Entries With Identical Sequence