SMTL ID : 7myd.1

Leishmania major dihydroorotate dehydrogenase in complex with 5-amino-2-(1H-pyrrol-1-yl)benzonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 30 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, L.106, S.132, N.162, K.199, I.228, N.229, S.230, G.256, G.257, V.260, C.283, G.284, G.285, V.286, V.305, G.306, T.307, A.308, Q.310 Ligands: GOL.5 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:V.56, A:Y.93, A:Y.93 Hydrogen bonds: A:K.78, A:S.79, A:S.79, A:S.79, A:N.162, A:K.199, A:I.228, A:G.257, A:G.285, A:G.306, A:T.307 Water bridges: A:A.54, A:N.102, A:N.229, A:N.229, A:N.229, A:G.284, A:G.284, A:V.286, A:V.286 FMN.7: 29 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, S.132, N.162, K.199, I.228, N.229, S.230, G.256, G.257, V.260, C.283, G.284, G.285, V.286, V.305, G.306, T.307, A.308, Q.310 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:V.56, B:Y.93, B:Y.93 Hydrogen bonds: B:K.78, B:S.79, B:S.79, B:S.79, B:N.162, B:K.199, B:I.228, B:G.257, B:G.284, B:G.285, B:G.306, B:T.307 Water bridges: B:N.229, B:N.229, B:N.229, B:G.284, B:V.286, B:V.286, B:V.286

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

SO4.2: 3 residues within 4Å: Chain A: N.43, H.194, S.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.43, A:S.195, A:S.195 Salt bridges: A:H.194 SO4.3: 2 residues within 4Å: Chain A: P.193, K.221 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.221 SO4.8: 3 residues within 4Å: Chain A: Q.250 Chain B: R.273, T.345 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.345, A:Q.250 Water bridges: B:R.273, B:R.273, B:T.345 Salt bridges: B:R.273

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: L.96, P.97, V.236, I.237, Y.259 Chain B: L.261, P.262, L.265, L.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.237 GOL.5: 4 residues within 4Å: Chain A: Y.93, M.104, Q.310 Ligands: FMN.1 No protein-ligand interaction detected (PLIP) GOL.9: 9 residues within 4Å: Chain A: L.261, P.262, L.265, L.294 Chain B: L.96, P.97, V.236, I.237, Y.259 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.237, B:I.237 Water bridges: B:Y.259

1 x SNQ: 5-azanyl-2-pyrrol-1-yl-benzenecarbonitrile(Non-covalent)

SNQ.6: 12 residues within 4Å: Chain A: Y.176, F.178, P.202, Y.203, F.204, H.208 Chain B: Y.176, D.177, F.178, Y.203, F.204, H.208 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.204, B:Y.176, B:F.178 Water bridges: A:H.208, B:H.208 pi-Stacking: A:Y.176, B:Y.176, B:H.208 Hydrogen bonds: B:Y.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pinheiro, M.P. et al., Leishmania major dihydroorotate dehydrogenase in complex with 5-amino-2-(1H-pyrrol-1-yl)benzonitrile. To Be Published

Release Date

2022-05-25

Peptides

Dihydroorotate dehydrogenase (fumarate): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Dihydroorotate dehydrogenase (fumarate)