SMTL ID : 3w1a.1

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-halogenated orotate derivatives

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: A.19, A.20, G.21, V.22, K.44, S.45, Y.59, N.68, M.70, N.128, K.165, V.194, N.195, S.196, G.222, G.223, I.226, C.249, G.250, G.251, G.272, T.273 Ligands: FOT.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.22, A:Y.59, A:Y.59 Hydrogen bonds: A:A.20, A:S.45, A:S.45, A:S.45, A:K.165, A:K.165, A:N.195, A:G.223, A:G.251, A:G.272, A:T.273, A:T.273 Water bridges: A:A.20, A:S.98, A:S.98, A:G.250, A:G.250, A:V.252, A:V.252 FMN.7: 23 residues within 4Å: Chain B: A.19, A.20, G.21, K.44, S.45, Y.59, N.68, M.70, N.128, K.165, V.194, N.195, S.196, G.222, G.223, I.226, C.249, G.250, G.251, V.271, G.272, T.273 Ligands: FOT.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.59, B:Y.59 Hydrogen bonds: B:A.20, B:S.45, B:S.45, B:S.45, B:K.165, B:K.165, B:N.195, B:G.223, B:G.251, B:G.272, B:T.273, B:T.273 Water bridges: B:A.20, B:S.98, B:G.250, B:G.250, B:V.252, B:V.252

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

NCO.2: 4 residues within 4Å: Chain A: Q.276, E.277, E.278, G.279 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.276, A:E.277, A:E.277, A:E.277

2 x FOT: 5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID(Non-covalent)

FOT.3: 13 residues within 4Å: Chain A: K.44, N.68, M.70, G.71, L.72, P.73, N.128, C.131, P.132, N.133, N.195, S.196 Ligands: FMN.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.68, A:N.68, A:M.70, A:G.71, A:L.72, A:N.128, A:N.133, A:N.195, A:N.195, A:S.196 Salt bridges: A:K.44 FOT.8: 14 residues within 4Å: Chain B: K.44, N.68, S.69, M.70, G.71, L.72, P.73, N.128, C.131, P.132, N.133, N.195, S.196 Ligands: FMN.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.68, B:N.68, B:N.68, B:M.70, B:G.71, B:L.72, B:N.128, B:N.133, B:N.195, B:N.195, B:S.196 Salt bridges: B:K.44

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: C.32, A.35, S.36, P.280 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.37, A:P.280 GOL.5: 6 residues within 4Å: Chain A: K.215, Q.216, F.218 Chain B: I.172, R.239, R.240 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.215, B:R.240, B:R.240 Water bridges: A:Q.216 GOL.6: 2 residues within 4Å: Chain A: D.176, T.177 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.176, A:T.177 GOL.9: 6 residues within 4Å: Chain A: I.172, R.239, R.240 Chain B: K.215, Q.216, F.218 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.216, B:Q.216 Hydrogen bonds: A:R.240, A:R.240 GOL.10: 2 residues within 4Å: Chain B: D.176, T.177 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.176, B:T.177 GOL.11: 4 residues within 4Å: Chain B: L.5, N.6, E.303, R.306 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.6, B:E.303, B:R.306 Water bridges: B:R.306, B:R.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inaoka, D.K. et al., Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-halogenated orotate derivatives. To be Published

Release Date

2013-11-13

Peptides

Dihydroorotate dehydrogenase (fumarate): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase (fumarate)

Related Entries With Identical Sequence