SMTL ID : 2e6d.1

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with fumarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

1 x NCO: COBALT HEXAMMINE(III)(Non-covalent)

NCO.1: 4 residues within 4Å: Chain A: Q.277, E.278, E.279, G.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.277, A:Q.277, A:E.278, A:E.278

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 22 residues within 4Å: Chain A: A.20, A.21, G.22, K.45, S.46, Y.60, N.69, M.71, N.129, K.166, V.195, N.196, S.197, G.223, G.224, I.227, C.250, G.251, G.252, G.273, T.274 Ligands: FUM.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.60, A:Y.60 Hydrogen bonds: A:A.21, A:S.46, A:S.46, A:S.46, A:K.166, A:K.166, A:N.196, A:G.224, A:G.252, A:G.273, A:T.274, A:T.274 Water bridges: A:S.99, A:L.222, A:G.251, A:G.251, A:V.253, A:V.253 FMN.7: 22 residues within 4Å: Chain B: A.20, A.21, G.22, K.45, S.46, Y.60, N.69, M.71, N.129, K.166, V.195, N.196, S.197, G.223, G.224, I.227, C.250, G.251, G.252, G.273, T.274 Ligands: FUM.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.60, B:Y.60 Hydrogen bonds: B:A.21, B:S.46, B:S.46, B:S.46, B:K.166, B:K.166, B:N.196, B:G.224, B:G.252, B:G.273, B:T.274, B:T.274 Water bridges: B:K.45, B:S.99, B:G.251, B:G.251, B:V.253, B:V.253

2 x FUM: FUMARIC ACID(Non-covalent)

FUM.3: 12 residues within 4Å: Chain A: K.45, N.69, M.71, G.72, L.73, P.74, N.129, C.132, P.133, N.134, N.196 Ligands: FMN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:M.71, A:G.72, A:L.73, A:N.129, A:N.134, A:N.196 Water bridges: A:N.69, A:S.197 Salt bridges: A:K.45 FUM.8: 12 residues within 4Å: Chain B: K.45, N.69, M.71, G.72, L.73, P.74, N.129, C.132, P.133, N.134, N.196 Ligands: FMN.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:M.71, B:G.72, B:L.73, B:N.129, B:N.134, B:N.196, B:S.197 Salt bridges: B:K.45

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: C.33, A.36, S.37, P.281 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.38, A:P.281 GOL.5: 6 residues within 4Å: Chain A: K.216, Q.217, F.219 Chain B: I.173, R.240, R.241 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.216, A:Q.217, B:R.241, B:R.241 GOL.6: 2 residues within 4Å: Chain A: D.177, T.178 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.177, A:T.178 GOL.9: 6 residues within 4Å: Chain A: I.173, R.240, R.241 Chain B: K.216, Q.217, F.219 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.217 Hydrogen bonds: A:R.241, A:R.241 GOL.10: 2 residues within 4Å: Chain B: D.177, T.178 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.177, B:T.178, B:T.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inaoka, D.K. et al., Structures of Trypanosoma cruzi dihydroorotate dehydrogenase complexed with substrates and products: atomic resolution insights into mechanisms of dihydroorotate oxidation and fumarate reduction. Biochemistry (2008)

Release Date

2008-01-15

Peptides

Dihydroorotate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase

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