SMTL ID : 7mx6.1

Leishmania major dihydroorotate dehydrogenase in complex with [4-(1H-pyrrol-1-yl)phenyl]methanol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 28 residues within 4Å: Chain A: A.20, A.21, G.22, V.23, K.45, S.46, Y.60, S.67, N.69, M.71, L.73, S.99, N.129, K.166, I.195, N.196, S.197, G.223, G.224, V.227, C.250, G.251, G.252, V.253, V.272, G.273, T.274, Q.277 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.23, A:Y.60, A:Y.60 Hydrogen bonds: A:K.45, A:S.46, A:S.46, A:S.46, A:N.129, A:K.166, A:I.195, A:N.196, A:G.224, A:G.251, A:G.252, A:G.273, A:T.274 Water bridges: A:A.21, A:N.69, A:V.253, A:V.253, A:V.253, A:Q.271 FMN.8: 28 residues within 4Å: Chain B: A.20, A.21, G.22, V.23, K.45, S.46, Y.60, S.67, N.69, M.71, L.73, S.99, N.129, K.166, I.195, N.196, S.197, G.223, G.224, V.227, C.250, G.251, G.252, V.253, V.272, G.273, T.274, Q.277 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:V.23, B:Y.60, B:Y.60 Hydrogen bonds: B:K.45, B:S.46, B:S.46, B:S.46, B:N.129, B:K.166, B:I.195, B:G.224, B:G.251, B:G.252, B:G.273, B:T.274 Water bridges: B:A.21, B:S.99, B:N.196, B:N.196, B:N.196, B:G.251, B:V.253, B:V.253, B:V.253, B:Q.271

1 x SNU: 4-(1H-pyrrol-1-yl)aniline(Non-covalent)

SNU.2: 12 residues within 4Å: Chain A: Y.143, F.145, P.169, Y.170, F.171, H.175 Chain B: Y.143, F.145, P.169, Y.170, F.171, H.175 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.143 Water bridges: A:H.175, B:H.175 pi-Stacking: A:Y.143, A:H.175, B:Y.143, B:H.175 Hydrophobic interactions: B:F.171

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

SO4.3: 2 residues within 4Å: Chain A: Y.239, R.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.239 Water bridges: A:R.307 SO4.4: 3 residues within 4Å: Chain A: N.10, H.161, S.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.10, A:S.162 Water bridges: A:S.162 Salt bridges: A:H.161 SO4.5: 2 residues within 4Å: Chain A: P.160, K.188 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.188 SO4.6: 7 residues within 4Å: Chain A: T.26, L.51, R.52, E.53, P.74, N.75, N.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.75, A:N.76 SO4.9: 3 residues within 4Å: Chain A: Q.217 Chain B: R.240, T.312 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.312, B:T.312 Water bridges: B:R.240, B:R.240, B:T.312 Salt bridges: B:R.240 SO4.13: 8 residues within 4Å: Chain B: Q.61, L.63, P.64, V.203, I.204, D.205, V.212 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.206

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain A: L.63, P.64, L.202, V.203, I.204, Y.226 Chain B: L.228, P.229, L.232, L.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.204 GOL.10: 10 residues within 4Å: Chain A: L.228, P.229, L.232, L.261 Chain B: L.63, P.64, V.203, I.204, Y.226 Ligands: SO4.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.204 GOL.11: 6 residues within 4Å: Chain A: K.298, Y.300, R.311 Chain B: E.207, T.208, E.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.207 Water bridges: B:E.209, B:E.209 GOL.12: 4 residues within 4Å: Chain B: T.120, P.160, H.161, S.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.161, B:S.162 Water bridges: B:S.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pinheiro, M.P. et al., Leishmania major dihydroorotate dehydrogenase in complex with [4-(1H-pyrrol-1-yl)phenyl]methanol. To be Published

Release Date

2022-05-18

Peptides

Dihydroorotate dehydrogenase (fumarate): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Dihydroorotate dehydrogenase (fumarate)