SMTL ID : 6fba.1

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor 2,3-naphthalenediol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: G.86, K.88 Chain B: G.86, K.88 Chain C: G.86, K.88 Ligands: SO4.8 7 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:G.86 Salt bridges: B:K.56, B:K.88, C:K.56, C:K.88, A:K.56, A:K.88 SO4.8: 9 residues within 4Å: Chain A: L.83, K.88 Chain B: L.83, S.87, K.88 Chain C: L.83, S.87, K.88 Ligands: SO4.1 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Salt bridges: B:K.88, C:K.88, A:K.88 Hydrogen bonds: C:S.87

3 x D48: naphthalene-2,3-diol(Non-covalent)

D48.2: 8 residues within 4Å: Chain A: E.104, A.109, I.112, L.113, Y.116 Chain B: R.73, L.298, P.299 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.112, A:I.112, A:L.113, A:L.113, A:Y.116, B:R.73 Water bridges: B:P.297 D48.9: 8 residues within 4Å: Chain B: E.104, A.109, I.112, L.113, Y.116 Chain C: R.73, L.298, P.299 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:R.73, C:R.73, B:I.112, B:I.112, B:L.113, B:L.113, B:Y.116 Hydrogen bonds: B:E.104 D48.12: 10 residues within 4Å: Chain A: R.73, C.76, L.298, P.299 Chain C: E.104, A.109, I.112, L.113, Y.116 Ligands: MLI.4 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.112, C:L.113, C:Y.116, A:R.73, A:R.73

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 6 residues within 4Å: Chain A: T.41, Q.44, F.45, I.48, Y.57, Y.332 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:F.45, A:Y.57 DMS.10: 5 residues within 4Å: Chain B: Q.44, F.45, I.48, Y.57, Y.332 3 PLIP interactions: 3 interactions with chain B pi-Cation interactions: B:F.45, B:Y.57, B:Y.332 DMS.13: 4 residues within 4Å: Chain C: Q.44, F.45, Y.57, Y.332 No protein-ligand interaction detected (PLIP)

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

MLI.4: 11 residues within 4Å: Chain A: R.73, T.74, S.77, Q.154, L.157, P.297, L.298, A.320, R.327 Chain C: Y.116 Ligands: D48.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.77, A:L.298 Water bridges: A:Q.154, A:R.327 Salt bridges: A:R.327 MLI.5: 6 residues within 4Å: Chain A: S.71, T.72, R.73, T.74, R.259 Chain C: K.102 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain A Salt bridges: C:K.102, A:R.73 Hydrophobic interactions: A:R.73 Hydrogen bonds: A:T.72, A:T.72, A:T.72, A:R.73, A:T.74 MLI.15: 6 residues within 4Å: Chain B: K.102 Chain C: P.70, S.71, T.72, R.73, T.74 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:P.70, C:T.72, C:R.73, C:T.74 Water bridges: C:R.73, C:R.123, B:K.102 Salt bridges: C:R.73, C:R.123, B:K.102

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: F.67, E.69, S.71, T.72, R.75, T.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.69, A:S.71, A:R.75 GOL.16: 3 residues within 4Å: Chain C: R.289, D.290, D.291 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.290, C:D.291, C:D.291

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

NA.7: 1 residues within 4Å: Chain C: V.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.89 Water bridges: A:N.91

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 8 residues within 4Å: Chain B: G.103, E.104, T.105, E.107, D.108 Chain C: R.300, V.301, V.306 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.300, B:T.105, B:T.105 Water bridges: C:R.300 PEG.14: 6 residues within 4Å: Chain A: V.306, D.309 Chain C: T.105, E.107, D.108, K.111 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.309, C:E.107 Water bridges: A:R.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lunev, S. et al., Identification of a non-competitive inhibitor of Plasmodium falciparum aspartate transcarbamoylase. Biochem. Biophys. Res. Commun. (2018)

Release Date

2018-02-21

Peptides

Aspartate transcarbamoylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Aspartate transcarbamoylase

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