SMTL ID : 3qjx.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 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: SER.5 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, SER.5

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

NA.2: 4 residues within 4Å: Chain A: S.353, D.354, G.356, R.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.353, A:R.358 Water bridges: A:D.354 NA.3: 1 residues within 4Å: Chain A: D.473 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.473, A:D.473 NA.4: 4 residues within 4Å: Chain A: E.142, M.281, N.394, Q.842 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.142 Water bridges: A:Q.842

1 x SER: SERINE(Non-covalent)

SER.5: 14 residues within 4Å: Chain A: E.142, M.281, A.283, M.284, E.285, H.318, E.319, H.322, K.340, E.341, Y.397, Y.402 Ligands: ZN.1, GOL.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.142, A:M.281 Water bridges: A:E.142 Salt bridges: A:H.318, A:H.322

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

MLI.6: 6 residues within 4Å: Chain A: R.662, E.663, T.666, R.707, F.711, A.743 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.711 Water bridges: A:R.662 Salt bridges: A:R.662, A:R.662, A:R.707

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: A.552, L.553, W.567, L.575, D.587, A.588, S.591 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.553, A:D.587, A:S.591, A:S.591 Water bridges: A:F.557 GOL.8: 8 residues within 4Å: Chain A: M.281, Y.397, T.398, L.399, Y.402, E.403, R.846 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.403, A:R.846 Water bridges: A:Y.402 GOL.9: 6 residues within 4Å: Chain A: V.85, P.91, W.92, T.93, W.95 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.85, A:W.92 GOL.10: 5 residues within 4Å: Chain A: L.82, V.83, S.84, W.95 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.82 GOL.11: 7 residues within 4Å: Chain A: Q.488, R.489, T.490, K.499, Q.500, P.501, A.536 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.488, A:T.490 GOL.12: 6 residues within 4Å: Chain A: W.246, E.313, L.355, V.691, E.692, H.693 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.691 Water bridges: A:N.253, A:H.693 GOL.13: 7 residues within 4Å: Chain A: M.281, G.282, R.314, H.318, Y.402 Ligands: SER.5, GOL.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Water bridges: A:R.314, A:H.318 Hydrogen bonds: S.5 GOL.14: 8 residues within 4Å: Chain A: N.280, M.281, G.282, K.295, Y.296, R.804 Ligands: GOL.13, GOL.18 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.282, A:N.293, A:K.295, A:Y.296, A:Y.296, A:R.804 Water bridges: A:N.801, A:R.804 GOL.15: 6 residues within 4Å: Chain A: T.305, K.307, D.308, L.735, K.769 Ligands: GOL.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.305 GOL.16: 3 residues within 4Å: Chain A: V.183, Q.198 Ligands: GOL.19 No protein-ligand interaction detected (PLIP) GOL.17: 6 residues within 4Å: Chain A: T.305, K.307, D.308, L.735, K.769 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.305, A:K.769 Water bridges: A:T.305 GOL.18: 5 residues within 4Å: Chain A: K.295, Y.296, R.804 Ligands: GOL.8, GOL.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.295, A:Y.296, A:R.804 GOL.19: 3 residues within 4Å: Chain A: V.183, Q.198 Ligands: GOL.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gumpena, R. et al., Discovery of alpha, beta- and alpha, gamma-Diamino Acid Scaffolds for the Inhibition of M1 Family Aminopeptidases. Chemmedchem (2011)

Release Date

2011-11-16

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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