SMTL ID : 3w2n.1

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-3-185

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

2 x ROD: 2,6-dioxo-5-{2-[2-(trifluoromethyl)phenyl]ethyl}-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid(Non-covalent)

ROD.1: 16 residues within 4Å: Chain A: K.44, R.51, N.68, S.69, M.70, G.71, L.72, S.100, L.102, N.128, C.131, P.132, N.195, S.196 Ligands: GOL.5, FMN.14 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.72, A:L.72, A:L.72, A:L.102, A:P.132 Hydrogen bonds: A:N.68, A:N.68, A:M.70, A:G.71, A:L.72, A:N.128, A:N.195, A:N.195, A:S.196 Salt bridges: A:K.44 Halogen bonds: A:R.51 ROD.16: 16 residues within 4Å: Chain B: K.44, N.68, S.69, M.70, G.71, L.72, S.100, L.102, N.128, S.130, C.131, P.132, N.195, S.196 Ligands: GOL.17, FMN.20 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.72, B:L.72, B:L.102 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.195, B:N.195, B:S.196 Salt bridges: B:K.44

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: C.32, A.35, S.36, P.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.280 Water bridges: A:S.37 GOL.3: 6 residues within 4Å: Chain A: I.172, R.239, R.240 Chain B: K.215, Q.216, F.218 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.240, A:R.240, B:Q.216 GOL.4: 6 residues within 4Å: Chain A: K.215, Q.216, F.218 Chain B: I.172, R.239, R.240 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.240, B:R.240 Water bridges: A:Q.216 GOL.5: 9 residues within 4Å: Chain A: S.130, Q.139, P.167, P.168, N.195, S.196, G.198, G.220 Ligands: ROD.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.130 Water bridges: A:S.196, A:G.198, A:N.199, A:G.220, A:G.220 GOL.6: 4 residues within 4Å: Chain A: F.62, V.202, I.203, D.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.204 GOL.7: 3 residues within 4Å: Chain A: Y.238, R.239, P.242 No protein-ligand interaction detected (PLIP) GOL.8: 5 residues within 4Å: Chain A: K.224, G.251, Y.253, D.257 Chain B: L.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.225 Hydrogen bonds: A:K.224 GOL.9: 5 residues within 4Å: Chain A: Y.142, F.144, H.174 Chain B: H.174 Ligands: GOL.19 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:H.174, B:H.174 Hydrogen bonds: B:H.174 GOL.10: 2 residues within 4Å: Chain A: V.108, R.112 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.109 GOL.11: 4 residues within 4Å: Chain A: V.22, L.23, D.29, Q.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.23, A:Q.276 Water bridges: A:C.24 GOL.12: 4 residues within 4Å: Chain A: L.5, N.6, E.303, R.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.6, A:R.306 GOL.13: 4 residues within 4Å: Chain A: F.144, E.145, R.148, T.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.148, A:R.148 GOL.17: 8 residues within 4Å: Chain B: S.130, Q.139, P.167, N.195, S.196, G.198, G.220 Ligands: ROD.16 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.130, B:S.130, B:S.196 Water bridges: B:G.198, B:N.199, B:G.220 GOL.18: 4 residues within 4Å: Chain B: Y.59, M.70, Q.276 Ligands: FMN.20 4 PLIP interactions: 4 interactions with chain B Water bridges: B:G.21, B:R.58, B:R.58, B:Q.276 GOL.19: 5 residues within 4Å: Chain A: H.174 Chain B: Y.142, F.144, H.174 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.142 Water bridges: B:H.174

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.14: 23 residues within 4Å: Chain A: A.19, A.20, G.21, K.44, S.45, Y.59, N.68, M.70, L.72, 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: ROD.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.59, A:Y.59 Hydrogen bonds: A:A.20, A:S.45, A:S.45, A:S.45, A:N.128, 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:S.98, A:G.250, A:V.252, A:V.252, A:V.252 FMN.20: 24 residues within 4Å: Chain B: A.19, A.20, G.21, K.44, S.45, Y.59, N.68, M.70, L.72, 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: ROD.16, GOL.18 21 PLIP interactions: 21 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:N.128, 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:K.44, B:S.98, B:G.250, B:G.250, B:V.252, B:V.252

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

NCO.15: 4 residues within 4Å: Chain A: Q.276, E.277, E.278, G.279 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.276, A:E.277, A:E.277 Water bridges: A:E.277, A:E.277, A:G.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inaoka, D.K. et al., Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-3-185. To be Published

Release Date

2013-12-04

Peptides

Dihydroorotate dehydrogenase (fumarate): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase (fumarate)

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