SMTL ID : 7s87.1

Crystal Structure of Dihydroorotate dehydrogenase from Plasmodium falciparum in complex with Orotate, FMN, and inhibitor NCGC00600348-01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

4 x 8IE: (4R)-3-methyl-5-[(4R)-4-methyl-3,4-dihydroisoquinolin-2(1H)-yl]thieno[2,3-e][1,2,4]triazolo[4,3-c]pyrimidine(Non-covalent)

8IE.1: 15 residues within 4Å: Chain A: Y.30, L.34, C.37, L.38, G.43, C.46, H.47, F.50, F.89, R.127, Y.360, L.363, V.364, G.367, M.368 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.34, A:L.38, A:H.47, A:F.89, A:V.364 Hydrogen bonds: A:R.127 8IE.7: 13 residues within 4Å: Chain A: S.22, F.27, L.29, Y.30, F.33, L.49, L.53 Chain B: Y.23, Y.30, L.49, L.53, I.58 Ligands: 8IE.8 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.29, A:F.33, A:F.33, A:F.33, A:L.49, A:L.53, B:L.49 8IE.8: 13 residues within 4Å: Chain A: Y.30, L.49, L.53, I.58 Chain B: S.22, F.27, L.29, Y.30, F.33, C.37, L.49, L.53 Ligands: 8IE.7 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.49, B:L.29, B:F.33, B:F.33, B:L.49, B:L.53 8IE.9: 13 residues within 4Å: Chain B: L.34, L.38, G.43, C.46, H.47, F.50, F.89, R.127, Y.360, L.363, V.364, G.367, M.368 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.34, B:L.38, B:H.47, B:F.89 Hydrogen bonds: B:R.127

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 24 residues within 4Å: Chain A: A.86, A.87, G.88, K.91, G.110, T.111, I.125, I.134, N.136, C.138, N.204, K.261, S.289, N.290, T.291, S.309, G.310, L.313, S.337, G.338, G.339, Y.360, S.361 Ligands: ORO.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.125, A:I.134, A:N.136, A:Y.360 Hydrogen bonds: A:A.87, A:K.91, A:T.111, A:T.111, A:T.111, A:N.204, A:K.261, A:K.261, A:N.290, A:S.309, A:G.310, A:S.337, A:G.338, A:G.339, A:Y.360, A:S.361 Water bridges: A:S.173, A:S.337, A:C.362 pi-Stacking: A:Y.360 FMN.10: 23 residues within 4Å: Chain B: A.86, A.87, G.88, K.91, G.110, T.111, I.125, N.136, N.204, S.206, K.261, S.289, N.290, T.291, S.309, G.310, L.313, S.337, G.338, G.339, Y.360, S.361 Ligands: ORO.11 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:I.125, B:N.136, B:Y.360 Hydrogen bonds: B:A.87, B:T.111, B:T.111, B:T.111, B:N.204, B:S.206, B:K.261, B:K.261, B:N.290, B:S.309, B:S.309, B:G.310, B:S.337, B:G.338, B:G.339, B:Y.360, B:S.361, B:S.361 Water bridges: B:S.173, B:G.338, B:I.340, B:I.340 pi-Stacking: B:Y.360

2 x ORO: OROTIC ACID(Non-covalent)

ORO.3: 12 residues within 4Å: Chain A: K.91, N.136, S.137, C.138, G.139, F.140, N.204, S.207, N.209, N.290, T.291 Ligands: FMN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.140 Hydrogen bonds: A:N.136, A:N.136, A:N.136, A:G.139, A:F.140, A:N.204, A:N.209, A:N.290, A:N.290, A:T.291 Water bridges: A:T.111 Salt bridges: A:K.91 ORO.11: 11 residues within 4Å: Chain B: N.136, C.138, G.139, F.140, N.204, S.207, P.208, N.209, N.290, T.291 Ligands: FMN.10 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.136, B:N.136, B:C.138, B:G.139, B:F.140, B:N.204, B:N.209, B:N.290, B:N.290, B:T.291 Salt bridges: B:K.91

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 2 residues within 4Å: Chain A: R.376, H.380 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.380

1 x P4K: polyethylene glycol(Non-covalent)

P4K.5: 9 residues within 4Å: Chain A: R.156, Q.159, E.160, S.166, F.246, F.249, N.250, T.251, K.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.253

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

SO4.6: 3 residues within 4Å: Chain A: I.125, F.126, R.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.127, A:R.127 Water bridges: A:R.127, A:R.127 Salt bridges: A:R.127 SO4.12: 4 residues within 4Å: Chain B: L.38, G.43, F.126, R.127 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.43, B:R.127, B:R.127 Salt bridges: B:R.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Crystal Structure of Dihydroorotate dehydrogenase from Plasmodium falciparum in complex with Orotate, FMN, and inhibitor NCGC00600348-01. To Be Published

Release Date

2021-09-29

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase (quinone), mitochondrial

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