SMTL ID : 6dwg.1

Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant Q139A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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, 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 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.284, 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:V.286, A:V.286 FMN.7: 22 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 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:G.257, B:G.284, B:G.285, B:G.306, B:T.307 Water bridges: B:K.78, B:E.160, B:N.162, B:N.229, B:V.286, B:V.286, B:V.286

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

SO4.2: 4 residues within 4Å: Chain A: L.96, P.97, D.238 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.238 Water bridges: A:A.239 SO4.3: 2 residues within 4Å: Chain A: R.273, T.345 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.345 Water bridges: A:T.345, A:T.345 Salt bridges: A:R.273 SO4.4: 3 residues within 4Å: Chain A: N.43, H.194, S.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.43, A:S.195 Salt bridges: A:H.194

4 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: SO4.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.237 Water bridges: A:Y.259, B:D.291 GOL.8: 6 residues within 4Å: Chain A: L.261, L.265, L.294 Chain B: V.236, I.237 Ligands: GOL.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.237 Water bridges: B:Y.259, A:D.291 GOL.9: 6 residues within 4Å: Chain A: P.172, N.233, K.249 Chain B: D.205, F.206, A.207 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.172, A:P.172, A:N.233, A:K.249, B:F.206, B:A.207 Water bridges: A:A.173 GOL.10: 3 residues within 4Å: Chain B: P.97, D.238 Ligands: GOL.8 No protein-ligand interaction detected (PLIP)

1 x NI: NICKEL (II) ION(Non-covalent)

NI.6: 2 residues within 4Å: Chain A: H.208 Chain B: H.208 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reis, R.A.G. et al., Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant Q139A. To Be Published

Release Date

2019-06-26

Peptides

Dihydroorotate dehydrogenase (fumarate): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase (fumarate)