SMTL ID : 3ebi.1

Structure of the M1 Alanylaminopeptidase from malaria complexed with the phosphinate dipeptide analog

Coordinates

PDB Format Compare

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.302, H.306, E.325 Ligands: BEY.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.302, A:H.306, A:E.325

1 x BEY: (2S)-3-[(R)-[(1S)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]-2-benzylpropanoic acid(Non-covalent)

BEY.2: 21 residues within 4Å: Chain A: Q.123, E.125, A.126, V.265, G.266, A.267, M.268, E.269, R.295, T.298, V.299, H.302, E.303, H.306, K.324, E.325, E.378, Y.381, Y.386, M.840 Ligands: ZN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.125, A:V.265, A:V.299, A:H.302, A:E.378, A:Y.381 Hydrogen bonds: A:G.266, A:E.269, A:K.324, A:Y.386 pi-Stacking: A:H.302, A:Y.381

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: K.285, Y.686, F.687, H.692, V.693, D.694, Q.697, M.698, R.701, Y.731 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.285, A:Y.686, A:D.694, A:D.694, A:R.701, A:R.701 Water bridges: A:Q.697, A:Y.731 GOL.5: 9 residues within 4Å: Chain A: D.351, Y.571, C.574, T.575, Y.578, Y.629, S.632, L.633, P.634 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.571, A:T.575 GOL.6: 5 residues within 4Å: Chain A: H.459, K.482, Y.547, N.641, F.642 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.549 GOL.7: 8 residues within 4Å: Chain A: V.265, G.266, N.277, N.279, S.280, R.295, N.800, R.803 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.277, A:N.279, A:S.280, A:R.295, A:N.800, A:R.803 Water bridges: A:G.266, A:Q.844 GOL.8: 5 residues within 4Å: Chain A: I.289, L.736, T.737, S.740, T.772 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.740, A:S.740 Water bridges: A:E.768, A:T.772

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain A: G.56 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.56, H2O.1, H2O.8, H2O.12, H2O.25 MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: E.763, N.798 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGowan, S. et al., Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-01-27

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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