SMTL ID : 8yhr.1

DHODH in complex with furocoumavirin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x ORO: OROTIC ACID(Non-covalent)

ORO.1: 11 residues within 4Å: Chain A: K.91, N.136, R.137, Y.138, G.139, F.140, N.203, N.275, T.276, G.294 Ligands: FMN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.140 Hydrogen bonds: A:N.136, A:N.136, A:N.136, A:Y.138, A:G.139, A:F.140, A:N.203, A:N.275, A:N.275, A:T.276 Water bridges: A:N.120 Salt bridges: A:K.91

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 30 residues within 4Å: Chain A: H.47, A.86, A.87, G.88, K.91, G.110, S.111, V.125, V.134, N.136, Y.138, F.140, N.172, N.203, K.246, T.274, N.275, T.276, S.296, G.297, L.300, V.324, G.325, G.326, V.327, L.346, Y.347, T.348 Ligands: ORO.1, 01.12 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:N.136, A:Y.138, A:Y.347 Hydrogen bonds: A:K.91, A:S.111, A:S.111, A:N.172, A:N.203, A:K.246, A:T.274, A:N.275, A:G.297, A:G.326, A:Y.347, A:T.348, A:T.348 Water bridges: A:A.87, A:G.325, A:G.325, A:V.327, A:V.327, A:Q.345

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: R.338, Q.372 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.338, A:R.338 GOL.4: 6 residues within 4Å: Chain A: Q.38, G.39, P.43, R.127, P.129, L.288 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.38, A:Q.38, A:R.127, A:R.127, A:R.127 Water bridges: A:R.127 GOL.5: 3 residues within 4Å: Chain A: T.23, G.24, D.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.24, A:D.25

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 8 residues within 4Å: Chain A: Q.159, A.160, T.163, L.169, L.196, A.197, D.198 Ligands: ACT.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.164 ACT.7: 4 residues within 4Å: Chain A: D.302, T.305, Q.306, R.309 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.302, A:Q.306 Salt bridges: A:R.309 ACT.8: 9 residues within 4Å: Chain A: H.77, A.197, D.198, R.237, V.238, H.239, R.240, P.241 Ligands: ACT.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.240, A:R.240 Salt bridges: A:H.77 ACT.9: 8 residues within 4Å: Chain A: E.44, H.47, R.48, V.51, K.91, H.92, Y.138, N.141 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.91 Hydrogen bonds: A:Y.138 Water bridges: A:H.47, A:R.48, A:H.92, A:N.141 Salt bridges: A:H.47, A:R.48 ACT.10: 2 residues within 4Å: Chain A: T.252, S.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.253 Water bridges: A:S.253, A:Q.254

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

SO4.11: 3 residues within 4Å: Chain A: R.236, V.238, H.239 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.236, A:H.239

1 x 01: 4-methyl-8-[(S)-oxidanyl(phenyl)methyl]-9-phenyl-furo[2,3-h]chromen-2-one

01.12: 23 residues within 4Å: Chain A: M.34, L.37, Q.38, L.41, P.43, A.46, H.47, A.50, F.53, T.54, L.59, F.89, M.102, V.125, R.127, V.134, Y.138, Y.347, L.350, T.351, G.354, P.355 Ligands: FMN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.37, A:Q.38, A:L.41, A:A.46, A:H.47, A:A.50, A:F.53, A:L.59, A:F.89, A:Y.347, A:P.355 Hydrogen bonds: A:L.350 Salt bridges: A:R.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakahara, M. et al., Structural and Functional Analyses of Inhibition of Human Dihydroorotate Dehydrogenase by Antiviral Furocoumavirin. Biochemistry (2024)

Release Date

2024-05-22

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial