SMTL ID : 3c3n.1

Crystal structure of dihydroorotate dehydrogenase from Trypanosoma cruzi strain Y

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: K.43, N.67, M.69, G.70, L.71, P.72, C.130, N.132 Ligands: FMN.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:M.69, A:G.70, A:L.71, A:N.132 Water bridges: A:N.67, A:N.67 Salt bridges: A:K.43 SO4.5: 9 residues within 4Å: Chain B: K.43, N.67, M.69, G.70, L.71, P.72, C.130, N.132 Ligands: FMN.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:M.69, B:G.70, B:L.71, B:N.132 Water bridges: B:N.67, B:N.127 Salt bridges: B:K.43 SO4.8: 9 residues within 4Å: Chain C: K.43, N.67, M.69, G.70, L.71, P.72, C.130, N.132 Ligands: FMN.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:M.69, C:G.70, C:L.71, C:N.132 Water bridges: C:N.67 Salt bridges: C:K.43 SO4.11: 9 residues within 4Å: Chain D: K.43, N.67, M.69, G.70, L.71, P.72, C.130, N.132 Ligands: FMN.12 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.67, D:G.70, D:L.71, D:N.132 Water bridges: D:N.127 Salt bridges: D:K.43

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 23 residues within 4Å: Chain A: A.18, A.19, G.20, K.43, S.44, Y.58, N.67, M.69, N.127, K.164, V.193, N.194, S.195, G.221, G.222, I.225, C.248, G.249, G.250, V.270, G.271, T.272 Ligands: SO4.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.58, A:Y.58 Hydrogen bonds: A:A.19, A:S.44, A:S.44, A:S.44, A:K.164, A:K.164, A:N.194, A:G.222, A:G.249, A:G.250, A:G.271, A:T.272 Water bridges: A:K.43, A:N.127, A:N.127, A:G.249, A:V.251, A:V.251, A:V.251 FMN.6: 24 residues within 4Å: Chain B: A.18, A.19, G.20, K.43, S.44, Y.58, S.65, N.67, M.69, N.127, K.164, V.193, N.194, S.195, G.221, G.222, I.225, C.248, G.249, G.250, V.270, G.271, T.272 Ligands: SO4.5 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.58, B:Y.58 Hydrogen bonds: B:A.19, B:S.44, B:S.44, B:S.44, B:K.164, B:K.164, B:N.194, B:S.195, B:G.222, B:G.249, B:G.250, B:V.251, B:G.271, B:T.272, B:T.272 Water bridges: B:A.19, B:K.43, B:S.97, B:S.97, B:N.127, B:N.127, B:G.249, B:A.273 FMN.9: 25 residues within 4Å: Chain C: A.18, A.19, G.20, V.21, K.43, S.44, Y.58, N.67, M.69, L.71, N.127, K.164, V.193, N.194, S.195, G.221, G.222, I.225, C.248, G.249, G.250, V.270, G.271, T.272 Ligands: SO4.8 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:V.21, C:Y.58, C:Y.58 Hydrogen bonds: C:A.19, C:S.44, C:S.44, C:S.44, C:K.164, C:K.164, C:N.194, C:G.222, C:G.249, C:G.250, C:G.271, C:T.272, C:T.272 Water bridges: C:K.43, C:S.97, C:N.127, C:N.127, C:L.220, C:G.249, C:V.251, C:A.273, C:A.273 FMN.12: 24 residues within 4Å: Chain D: A.18, A.19, G.20, V.21, K.43, S.44, Y.58, N.67, M.69, N.127, K.164, V.193, N.194, S.195, G.221, G.222, I.225, C.248, G.249, G.250, V.270, G.271, T.272 Ligands: SO4.11 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:V.21, D:Y.58, D:Y.58 Hydrogen bonds: D:A.19, D:S.44, D:S.44, D:S.44, D:K.164, D:K.164, D:N.194, D:S.195, D:G.222, D:G.249, D:G.250, D:G.271, D:T.272 Water bridges: D:A.19, D:S.97, D:N.127, D:N.127, D:V.251, D:V.251, D:A.273, D:A.273

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.214, Q.215, F.217 Chain D: I.171, A.235, R.239 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.239, D:R.239 GOL.4: 9 residues within 4Å: Chain A: Y.168, F.169, D.170, H.173 Chain D: Y.141, Y.168, F.169, D.170, H.173 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:F.169, A:D.170, A:H.173, D:F.169, D:D.170 GOL.7: 8 residues within 4Å: Chain B: Y.168, F.169, H.173 Chain C: Y.141, Y.168, F.169, D.170, H.173 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:F.169, C:D.170, C:H.173, B:F.169, B:H.173 GOL.10: 7 residues within 4Å: Chain B: K.214, Q.215, F.217 Chain C: I.171, A.235, R.238, R.239 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.239, C:R.239, B:K.214 GOL.13: 2 residues within 4Å: Chain A: D.203 Chain D: E.255 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.255

Links

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Citation

Pinheiro, M.P. et al., Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase from Y strain. Biochem.Biophys.Res.Commun. (2008)

Release Date

2008-04-29

Peptides

Dihydroorotate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dihydroorotate dehydrogenase