SMTL ID : 4ef8.1

Crystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with Phenyl isothiocyanate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 22 residues within 4Å: Chain A: A.53, A.54, G.55, K.78, S.79, Y.93, N.102, M.104, N.162, K.199, I.228, N.229, S.230, G.256, G.257, V.260, C.283, G.284, G.285, V.305, G.306, T.307 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.93, A:Y.93 Hydrogen bonds: A:A.54, A:S.79, A:S.79, A:S.79, A:K.199, A:K.199, A:N.229, A:G.257, A:G.284, A:G.285, A:G.306, A:T.307, A:T.307 Water bridges: A:K.78, A:K.78, A:N.162, A:N.162, A:G.284, A:V.286, A:V.286 FMN.7: 22 residues within 4Å: Chain B: A.53, A.54, G.55, K.78, S.79, Y.93, N.102, M.104, N.162, K.199, I.228, N.229, S.230, G.256, G.257, V.260, C.283, G.284, G.285, V.305, G.306, T.307 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.93, B:Y.93 Hydrogen bonds: B:A.54, B:S.79, B:S.79, B:S.79, B:K.199, B:K.199, B:N.229, B:G.257, B:G.284, B:G.285, B:G.306, B:T.307 Water bridges: B:K.78, B:K.78, B:N.162, B:N.162, B:G.284, B:V.286, B:V.286

2 x 0FI: N-phenylthioformamide(Covalent)

0FI.2: 11 residues within 4Å: Chain A: G.135, L.136, S.137, M.138, N.141, C.165, P.166, N.167, V.174, C.184, V.188 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.174 Hydrogen bonds: A:S.137, A:N.141 0FI.6: 11 residues within 4Å: Chain B: G.135, L.136, S.137, M.138, N.141, C.165, P.166, N.167, V.174, C.184, V.188 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.174 Hydrogen bonds: B:S.137, B:N.141

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

SO4.3: 3 residues within 4Å: Chain A: P.193, H.194, S.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.195 Salt bridges: A:H.194 SO4.8: 3 residues within 4Å: Chain B: S.137, M.138, R.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.138, B:R.139

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Y.176, F.178, H.208 Chain B: H.208 Ligands: GOL.9 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.176, A:Y.176, A:Y.176, A:H.208, B:H.208 GOL.5: 6 residues within 4Å: Chain A: P.97, V.236, I.237 Chain B: L.261, L.265, L.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.237 Water bridges: A:Y.259 GOL.9: 5 residues within 4Å: Chain A: H.208 Chain B: Y.176, F.178, H.208 Ligands: GOL.4 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.176, B:Y.176, B:Y.176, B:H.208, A:H.208 GOL.10: 6 residues within 4Å: Chain A: L.261, L.265, L.294 Chain B: P.97, V.236, I.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pinheiro, M.P. et al., Target sites for the design of anti-trypanosomatid drugs based on the structure of dihydroorotate dehydrogenase. Curr.Pharm.Des. (2013)

Release Date

2012-12-12

Peptides

Dihydroorotate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase

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