SMTL ID : 1tv5.2 (1 other biounit)

Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: K.67, Y.68 Chain B: K.67, Y.68 Chain C: K.67, Y.68 Ligands: SO4.7, SO4.13 7 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:Y.68, B:Y.68, C:Y.68, A:Y.68 Salt bridges: B:K.67, C:K.67, A:K.67 SO4.7: 8 residues within 4Å: Chain A: K.67, Y.68 Chain B: K.67, Y.68 Chain C: K.67, Y.68 Ligands: SO4.1, SO4.13 7 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:Y.68, C:Y.68, C:Y.68, A:Y.68 Salt bridges: B:K.67, C:K.67, A:K.67 SO4.13: 8 residues within 4Å: Chain A: K.67, Y.68 Chain B: K.67, Y.68 Chain C: K.67, Y.68 Ligands: SO4.1, SO4.7 7 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: B:Y.68, C:Y.68, A:Y.68, A:Y.68 Salt bridges: B:K.67, C:K.67, A:K.67

3 x A26: (2Z)-2-cyano-3-hydroxy-N-[4-(trifluoromethyl)phenyl]but-2-enamide(Non-covalent)

A26.2: 13 residues within 4Å: Chain A: F.45, L.46, G.55, H.59, F.62, F.101, I.137, R.139, Y.402, V.406, G.409, M.410 Ligands: FMN.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.46, A:H.59, A:F.62, A:F.62, A:I.137, A:R.139, A:V.406 Hydrogen bonds: A:H.59, A:R.139 A26.8: 13 residues within 4Å: Chain B: F.45, L.46, G.55, H.59, F.62, F.101, I.137, R.139, Y.402, V.406, G.409, M.410 Ligands: FMN.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.46, B:H.59, B:F.62, B:F.62, B:I.137, B:R.139, B:V.406 Hydrogen bonds: B:H.59, B:R.139 A26.14: 13 residues within 4Å: Chain C: F.45, L.46, G.55, H.59, F.62, F.101, I.137, R.139, Y.402, V.406, G.409, M.410 Ligands: FMN.15 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.46, C:H.59, C:F.62, C:F.62, C:I.137, C:R.139, C:V.406 Hydrogen bonds: C:H.59, C:R.139

3 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 26 residues within 4Å: Chain A: A.98, A.99, G.100, K.103, G.122, T.123, I.137, I.146, N.148, C.150, S.185, N.216, K.303, S.331, N.332, T.333, S.351, G.352, L.355, S.379, G.380, G.381, Y.402, S.403 Ligands: A26.2, ORO.4 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.137, A:I.146, A:N.148, A:Y.402 Hydrogen bonds: A:A.99, A:K.103, A:T.123, A:S.185, A:N.216, A:K.303, A:K.303, A:N.332, A:S.351, A:G.352, A:S.379, A:G.380, A:G.381, A:Y.402, A:S.403, A:S.403 Water bridges: A:A.99, A:T.123, A:I.382, A:I.382, A:I.382, A:Q.400 pi-Stacking: A:Y.402 FMN.9: 26 residues within 4Å: Chain B: A.98, A.99, G.100, K.103, G.122, T.123, I.137, I.146, N.148, C.150, S.185, N.216, K.303, S.331, N.332, T.333, S.351, G.352, L.355, S.379, G.380, G.381, Y.402, S.403 Ligands: A26.8, ORO.10 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:I.137, B:I.146, B:N.148, B:Y.402 Hydrogen bonds: B:A.99, B:K.103, B:T.123, B:S.185, B:N.216, B:K.303, B:K.303, B:N.332, B:S.351, B:G.352, B:S.379, B:G.380, B:G.381, B:Y.402, B:S.403, B:S.403 Water bridges: B:A.99, B:T.123, B:I.382, B:I.382, B:I.382, B:Q.400 pi-Stacking: B:Y.402 FMN.15: 26 residues within 4Å: Chain C: A.98, A.99, G.100, K.103, G.122, T.123, I.137, I.146, N.148, C.150, S.185, N.216, K.303, S.331, N.332, T.333, S.351, G.352, L.355, S.379, G.380, G.381, Y.402, S.403 Ligands: A26.14, ORO.16 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:I.137, C:I.146, C:N.148, C:Y.402 Hydrogen bonds: C:A.99, C:K.103, C:T.123, C:S.185, C:N.216, C:K.303, C:K.303, C:N.332, C:S.351, C:G.352, C:S.379, C:G.380, C:G.381, C:Y.402, C:S.403, C:S.403 Water bridges: C:A.99, C:T.123, C:I.382, C:I.382, C:I.382, C:Q.400 pi-Stacking: C:Y.402

3 x ORO: OROTIC ACID(Non-covalent)

ORO.4: 11 residues within 4Å: Chain A: K.103, N.148, C.150, G.151, F.152, N.216, S.219, N.221, N.332, T.333 Ligands: FMN.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.152 Hydrogen bonds: A:N.148, A:N.148, A:G.151, A:F.152, A:N.216, A:S.219, A:N.221, A:N.332, A:N.332 Salt bridges: A:K.103 ORO.10: 11 residues within 4Å: Chain B: K.103, N.148, C.150, G.151, F.152, N.216, S.219, N.221, N.332, T.333 Ligands: FMN.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.152 Hydrogen bonds: B:N.148, B:N.148, B:G.151, B:F.152, B:N.216, B:S.219, B:N.221, B:N.332, B:N.332 Salt bridges: B:K.103 ORO.16: 11 residues within 4Å: Chain C: K.103, N.148, C.150, G.151, F.152, N.216, S.219, N.221, N.332, T.333 Ligands: FMN.15 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.152 Hydrogen bonds: C:N.148, C:N.148, C:G.151, C:F.152, C:N.216, C:S.219, C:N.221, C:N.332, C:N.332 Salt bridges: C:K.103

6 x N8E: 3,6,9,12,15-PENTAOXATRICOSAN-1-OL(Non-covalent)

N8E.5: 4 residues within 4Å: Chain A: D.43, I.44, L.46, K.47 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.44 Hydrogen bonds: A:K.47 N8E.6: 9 residues within 4Å: Chain A: I.44, F.45, F.48, L.65, I.70 Chain B: F.48, I.53, I.57, L.61 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.44, A:F.48 Water bridges: A:Y.42 N8E.11: 4 residues within 4Å: Chain B: D.43, I.44, L.46, K.47 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.44 Hydrogen bonds: B:K.47 N8E.12: 9 residues within 4Å: Chain B: I.44, F.45, F.48, L.65, I.70 Chain C: F.48, I.53, I.57, L.61 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.44, B:F.48 Water bridges: B:Y.42 N8E.17: 4 residues within 4Å: Chain C: D.43, I.44, L.46, K.47 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.44 Hydrogen bonds: C:K.47 N8E.18: 9 residues within 4Å: Chain A: F.48, I.53, I.57, L.61 Chain C: I.44, F.45, F.48, L.65, I.70 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.44, C:F.48 Water bridges: C:Y.42

Links

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Citation

Hurt, D.E. et al., Structure of Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor. Acta Crystallogr.,Sect.D (2006)

Release Date

2005-09-06

Peptides

Dihydroorotate dehydrogenase homolog, mitochondrial: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Dihydroorotate dehydrogenase homolog, mitochondrial

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