SMTL ID : 3qvi.3 (2 other biounits)

Crystal structure of KNI-10395 bound histo-aspartic protease (HAP) from Plasmodium falciparum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x K95: (4R)-N-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]-3-[(2S,3S)-2-HYDROXY-3-{[S-METHYL-N-(PHENYLACETYL)-L-CYSTEINYL]AMINO}-4-PHENYLBUTANOYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXAMIDE(Non-covalent)

K95.1: 13 residues within 4Å: Chain A: H.157, A.159, S.160, W.164, L.254, M.315, I.335, D.337, E.418 Chain B: E.401, F.404, A.406, L.407 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:W.164, A:I.335, B:L.407, B:L.407 Hydrogen bonds: A:A.159, B:E.401 Water bridges: B:E.401, B:A.406, B:L.407 pi-Stacking: B:F.404 K95.2: 15 residues within 4Å: Chain A: E.401, F.404, A.406, L.407 Chain B: H.157, A.159, S.160, W.164, L.198, V.246, L.254, M.315, D.337, L.417 Ligands: EDO.10 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.404, A:F.404, A:A.406, A:L.407, B:W.164, B:L.198, B:V.246, B:L.417 Hydrogen bonds: A:E.401, B:A.159 Water bridges: A:L.407

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: S.161, Y.223, G.248, L.249, G.250, P.261, Y.262, Y.438 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.223, A:G.250, A:G.250, A:Y.262, A:I.263 Water bridges: A:Y.223 EDO.4: 3 residues within 4Å: Chain A: Q.269, N.270, K.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.271 EDO.5: 4 residues within 4Å: Chain A: L.213, S.220, P.222, K.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.271 EDO.6: 5 residues within 4Å: Chain A: D.192, T.194, F.209, K.224, G.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.224, A:G.257 Water bridges: A:D.192, A:D.192 EDO.8: 7 residues within 4Å: Chain A: F.237 Chain B: P.399, E.401, N.402, I.403, F.404, S.405 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.405 Water bridges: B:F.404, A:S.241 EDO.9: 4 residues within 4Å: Chain B: E.348, N.351, Q.352, E.355 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.348, B:E.355, B:E.355 Water bridges: B:Q.352 EDO.10: 6 residues within 4Å: Chain B: S.160, S.161, N.162, W.164, L.254 Ligands: K95.2 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.161, B:N.162, B:N.162 Water bridges: B:A.159, B:S.160 EDO.11: 1 residues within 4Å: Chain B: N.148 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.148

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

NA.7: 2 residues within 4Å: Chain B: R.383 Ligands: PG4.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.383

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 8 residues within 4Å: Chain B: D.319, L.320, D.321, K.331, R.383, S.384, P.385 Ligands: NA.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhaumik, P. et al., Structural insights into the activation and inhibition of histo-aspartic protease from Plasmodium falciparum. Biochemistry (2011)

Release Date

2011-10-12

Peptides

Histo-aspartic protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Histo-aspartic protease

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