SMTL ID : 4ef9.1

Crystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with 4-Nitrophenyl isothiocyanate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x 4NF: N-(4-nitrophenyl)thioformamide(Covalent)

4NF.1: 8 residues within 4Å: Chain A: G.135, L.136, S.137, M.138, N.141, K.171, V.174, C.184 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.174, A:V.174 Hydrogen bonds: A:S.137, A:N.141 4NF.9: 9 residues within 4Å: Chain B: G.135, L.136, S.137, M.138, N.141, K.171, P.172, V.174, C.184 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.174, B:V.174 Water bridges: B:M.138

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 24 residues within 4Å: Chain A: A.53, A.54, G.55, V.56, 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 Ligands: SO4.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.56, 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.285, A:G.306, A:T.307, A:T.307 Water bridges: A:K.78, A:N.162, A:N.162, A:G.284, A:G.284, A:V.286, A:V.286 FMN.10: 23 residues within 4Å: Chain B: A.53, A.54, G.55, V.56, 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, G.306, T.307 Ligands: SO4.11 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.56, 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:N.162, B:N.162, B:G.284, B:V.286, B:V.286

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

SO4.3: 9 residues within 4Å: Chain A: K.78, N.102, M.104, G.105, L.106, P.107, C.165, N.167 Ligands: FMN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.105, A:L.106, A:N.167 Water bridges: A:N.102, A:N.229 Salt bridges: A:K.78 SO4.4: 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 SO4.6: 5 residues within 4Å: Chain A: T.59, R.85, P.107, N.108, N.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.109 SO4.7: 2 residues within 4Å: Chain A: Y.93, M.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.310 Water bridges: A:R.92, A:Y.93 SO4.8: 6 residues within 4Å: Chain A: L.96, P.97, V.236, I.237, D.238 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.237 Water bridges: A:Q.94, A:A.239, A:A.239 SO4.11: 9 residues within 4Å: Chain B: K.78, N.102, M.104, G.105, L.106, P.107, C.165, N.167 Ligands: FMN.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.105, B:L.106, B:N.167 Water bridges: B:N.102, B:N.229, B:N.229 Salt bridges: B:K.78 SO4.13: 5 residues within 4Å: Chain B: T.59, R.85, P.107, N.108, N.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.85

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: V.236, I.237 Chain B: L.261, L.265, L.294 Ligands: SO4.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:D.291, A:Y.259 Hydrogen bonds: A:I.237 GOL.12: 5 residues within 4Å: Chain A: L.261, L.265, L.294 Chain B: V.236, I.237 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.237 Water bridges: 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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