SMTL ID : 3tq0.1

Crystal structure of Leishmania major dihydroorotate dehydrogenase in complex with fumarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 25 residues within 4Å: Chain A: A.53, A.54, G.55, V.56, K.78, S.79, Y.93, S.100, 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: FUM.2 21 PLIP interactions: 21 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:A.54, A:G.284, A:V.286, A:V.286, A:V.286 FMN.9: 26 residues within 4Å: Chain B: A.53, A.54, G.55, V.56, K.78, S.79, Y.93, S.100, N.102, M.104, L.106, 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: FUM.10 22 PLIP interactions: 22 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:A.54, B:S.132, B:S.132, B:G.284, B:V.286, B:V.286, B:V.286

2 x FUM: FUMARIC ACID(Non-covalent)

FUM.2: 13 residues within 4Å: Chain A: K.78, N.102, M.104, G.105, L.106, P.107, N.162, S.164, C.165, P.166, N.167, N.229 Ligands: FMN.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.102, A:M.104, A:G.105, A:L.106, A:N.162, A:N.167, A:N.229, A:S.230 Salt bridges: A:K.78, A:K.199 FUM.10: 13 residues within 4Å: Chain B: K.78, N.102, M.104, G.105, L.106, P.107, N.162, S.164, C.165, P.166, N.167, N.229 Ligands: FMN.9 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:M.104, B:G.105, B:L.106, B:N.162, B:N.167, B:N.229 Salt bridges: B:K.78, B:K.199

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: V.236, I.237, Y.259 Chain B: L.261, L.265, L.294 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.237 Water bridges: A:Y.259, A:Y.259, B:D.291 GOL.11: 5 residues within 4Å: Chain A: L.261, L.265, L.294 Chain B: V.236, I.237 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

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

NI.4: 2 residues within 4Å: Chain B: Y.176, H.208 No protein-ligand interaction detected (PLIP)

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

SO4.5: 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: 2 residues within 4Å: Chain A: P.193, K.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.193 Salt bridges: A:K.221 SO4.7: 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:R.273, A:T.345 Salt bridges: A:R.273 SO4.8: 2 residues within 4Å: Chain A: Y.272, R.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cordeiro, A.T. et al., Crystal structure of dihydroorotate dehydrogenase from Leishmania major. Biochimie (2012)

Release Date

2012-05-16

Peptides

Dihydroorotate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase

Related Entries With Identical Sequence