SMTL ID : 2b4g.1 (1 other biounit)

dihydroorotate dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

6 x BR: BROMIDE ION(Non-covalent)

BR.1: 5 residues within 4Å: Chain A: P.136, Q.143, N.203 Chain B: D.175, I.176 Ligand excluded by PLIP BR.2: 3 residues within 4Å: Chain A: Y.173, F.174, H.178 Ligand excluded by PLIP BR.3: 3 residues within 4Å: Chain A: P.142 Chain B: I.176, A.177 Ligand excluded by PLIP BR.4: 3 residues within 4Å: Chain A: L.12, P.165, K.193 Ligand excluded by PLIP BR.9: 3 residues within 4Å: Chain A: I.176 Chain B: G.140, P.142 Ligand excluded by PLIP BR.10: 1 residues within 4Å: Chain B: N.300 Ligand excluded by PLIP

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 23 residues within 4Å: Chain A: A.23, A.24, G.25, K.48, S.49, Y.63, N.72, M.74, N.132, K.169, V.198, N.199, S.200, G.226, G.227, V.230, C.253, G.254, G.255, V.275, G.276, T.277 Ligands: ORO.6 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.63, A:Y.63 Hydrogen bonds: A:A.24, A:S.49, A:S.49, A:S.49, A:K.169, A:K.169, A:N.199, A:G.227, A:G.255, A:G.276, A:T.277, A:T.277 Water bridges: A:A.24, A:G.254, A:G.254, A:V.256, A:V.256 FMN.11: 23 residues within 4Å: Chain B: A.23, A.24, G.25, K.48, S.49, Y.63, N.72, M.74, N.132, K.169, V.198, N.199, S.200, G.226, G.227, V.230, C.253, G.254, G.255, V.275, G.276, T.277 Ligands: ORO.12 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.63, B:Y.63 Hydrogen bonds: B:A.24, B:S.49, B:S.49, B:S.49, B:K.169, B:K.169, B:N.199, B:G.227, B:G.255, B:G.276, B:T.277 Water bridges: B:G.254, B:G.254, B:V.256, B:V.256

2 x ORO: OROTIC ACID(Non-covalent)

ORO.6: 14 residues within 4Å: Chain A: K.48, N.72, S.73, M.74, G.75, L.76, P.77, N.132, C.135, P.136, N.137, N.199, S.200 Ligands: FMN.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.76 Hydrogen bonds: A:N.72, A:N.72, A:N.72, A:M.74, A:G.75, A:L.76, A:N.132, A:N.137, A:N.199, A:N.199, A:S.200 Salt bridges: A:K.48 ORO.12: 14 residues within 4Å: Chain B: K.48, N.72, S.73, M.74, G.75, L.76, P.77, N.132, C.135, P.136, N.137, N.199, S.200 Ligands: FMN.11 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.76 Hydrogen bonds: B:N.72, B:N.72, B:N.72, B:M.74, B:G.75, B:L.76, B:N.132, B:N.137, B:N.199, B:N.199, B:S.200 Salt bridges: B:K.48

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: I.176, R.243, R.244 Chain B: K.219, Q.220, F.222 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.244, A:R.244, B:K.219 Water bridges: B:Q.220 GOL.8: 1 residues within 4Å: Chain A: D.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.281 Water bridges: A:D.281, A:D.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arakaki, T.L. et al., Characterization of Trypanosoma brucei dihydroorotate dehydrogenase as a possible drug target; structural, kinetic and RNAi studies. Mol.Microbiol. (2008)

Release Date

2005-10-11

Peptides

dihydroorotate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

dihydroorotate dehydrogenase

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