SMTL ID : 3q43.1

X-ray crystal structure of PfA-M1 bound to bestatin derivative 15

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.302, E.303, H.306, E.325 Ligands: D66.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.302, A:H.306, A:E.325, A:E.325

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: E.763 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain A: G.56 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.56 MG.5: 1 residues within 4Å: Chain A: D.244 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: H.349 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.349

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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:N.279, A:S.280, A:R.295, A:R.295, A:R.803 Water bridges: A:Q.844 GOL.6: 8 residues within 4Å: Chain A: D.351, Y.571, C.574, T.575, Y.578, Y.629, S.632, P.634 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.629 Water bridges: A:D.351, A:Q.635 GOL.8: 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, A:Y.731 Water bridges: A:Y.731 GOL.9: 5 residues within 4Å: Chain A: H.459, K.482, Y.547, N.641, F.642 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.482, A:Y.547, A:E.549 Water bridges: A:E.549

1 x D66: N-[(2S,3R)-3-amino-2-hydroxy-4-(4-methoxyphenyl)butanoyl]-L-leucine(Non-covalent)

D66.10: 19 residues within 4Å: Chain A: Q.123, E.125, 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 Ligands: ZN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.125, A:V.265, A:T.298, A:V.299, A:H.302, A:Y.381 Hydrogen bonds: A:E.125, A:G.266, A:A.267, A:A.267, A:E.303, A:K.324, A:Y.386 Water bridges: A:R.295 Salt bridges: A:R.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Velmourougane, G. et al., Synthesis of new (-)-bestatin-based inhibitor libraries reveals a novel binding mode in the s1 pocket of the essential malaria m1 metalloaminopeptidase. J.Med.Chem. (2011)

Release Date

2011-03-16

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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