SMTL ID : 5ue9.2 (1 other biounit)

WT DHODB with orotate bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

hetero-2-2-mer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 20 residues within 4Å: Chain A: L.51, R.52, R.53, P.54, I.55, S.56, L.70, Y.71, R.72, G.74, S.78, G.79, T.80, I.120, M.220, E.221, S.222, R.223, M.224, P.253 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.54, A:E.221, A:E.221, A:P.253 Hydrogen bonds: A:R.52, A:P.54, A:S.56, A:L.70, A:R.72, A:G.74, A:S.78, A:G.79, A:T.80, A:T.80, A:R.223 Water bridges: A:S.56, A:E.221, B:E.61 Salt bridges: A:R.53, A:R.53 pi-Cation interactions: A:R.223 FAD.6: 20 residues within 4Å: Chain C: L.51, R.52, R.53, P.54, I.55, S.56, L.70, Y.71, R.72, G.74, S.78, G.79, T.80, I.120, M.220, E.221, S.222, R.223, M.224, P.253 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:P.54, C:E.221, C:E.221, C:P.253 Hydrogen bonds: C:R.52, C:P.54, C:S.56, C:L.70, C:R.72, C:G.74, C:S.78, C:G.79, C:T.80, C:T.80, C:R.223 Water bridges: C:S.56, C:S.56, D:E.61 Salt bridges: C:R.53, C:R.53 pi-Cation interactions: C:R.223

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 12 residues within 4Å: Chain A: M.224, A.225, C.226, G.227, G.229, A.230, C.231, Y.232, A.233, C.234, K.247, C.249 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.226, A:C.231, A:C.234, A:C.249 FES.7: 12 residues within 4Å: Chain C: M.224, A.225, C.226, G.227, G.229, A.230, C.231, Y.232, A.233, C.234, K.247, C.249 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.226, C:C.231, C:C.234, C:C.249

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 23 residues within 4Å: Chain B: A.19, S.20, G.21, C.22, K.44, A.45, N.68, I.70, N.100, N.128, K.166, I.192, N.193, T.194, S.217, G.218, M.243, G.244, G.245, V.265, G.266, T.267 Ligands: ORO.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.70 Hydrogen bonds: B:S.20, B:S.20, B:A.45, B:N.100, B:N.100, B:K.166, B:K.166, B:N.193, B:S.217, B:G.218, B:G.245, B:G.266, B:T.267, B:T.267 Water bridges: B:G.244, B:V.246 FMN.8: 23 residues within 4Å: Chain D: A.19, S.20, G.21, C.22, K.44, A.45, N.68, I.70, N.100, N.128, K.166, I.192, N.193, T.194, S.217, G.218, M.243, G.244, G.245, V.265, G.266, T.267 Ligands: ORO.9 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.70 Hydrogen bonds: D:S.20, D:S.20, D:A.45, D:N.100, D:N.100, D:K.166, D:K.166, D:N.193, D:S.217, D:G.218, D:G.245, D:G.266, D:T.267 Water bridges: D:G.244, D:V.246

2 x ORO: OROTIC ACID(Non-covalent)

ORO.4: 10 residues within 4Å: Chain B: K.44, N.68, A.69, I.70, G.71, L.72, N.128, N.193, T.194 Ligands: FMN.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.72 Hydrogen bonds: B:N.68, B:N.68, B:I.70, B:G.71, B:L.72, B:N.128, B:N.193, B:N.193 Salt bridges: B:K.44 ORO.9: 10 residues within 4Å: Chain D: K.44, N.68, A.69, I.70, G.71, L.72, N.128, N.193, T.194 Ligands: FMN.8 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.72 Hydrogen bonds: D:N.68, D:N.68, D:I.70, D:G.71, D:L.72, D:N.128, D:N.193, D:N.193, D:T.194 Salt bridges: D:K.44

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: N.243, H.244, A.245 Chain B: R.51, F.52, Q.73, N.74, P.75 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.245, B:N.74 GOL.10: 8 residues within 4Å: Chain C: N.243, H.244, A.245 Chain D: R.51, F.52, Q.73, N.74, P.75 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.245, D:N.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pompeu, Y.A. et al., Isoleucine 74 Plays a Key Role in Controlling Electron Transfer Between Lactococcus lactis Dihydroorotate Dehydrogenase 1B Subunits. to be published

Release Date

2017-09-06

Peptides

Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit: AC
Dihydroorotate dehydrogenase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
D

B
C

D
C

Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit

Dihydroorotate dehydrogenase

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