SMTL ID : 1ep2.1

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B COMPLEXED WITH OROTATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: A.23, S.24, G.25, C.26, K.48, A.49, N.72, N.104, N.132, K.170, I.196, N.197, T.198, S.221, G.222, M.247, G.248, G.249, G.270, T.271 Ligands: ORO.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:A.49, A:N.104, A:N.104, A:K.170, A:K.170, A:N.197, A:S.221, A:G.222, A:G.248, A:G.249, A:G.270, A:T.271 Water bridges: A:S.24, A:K.48, A:V.250, A:V.250 FMN.5: 21 residues within 4Å: Chain C: A.23, S.24, G.25, C.26, K.48, A.49, N.72, N.104, N.132, K.170, I.196, N.197, T.198, S.221, G.222, M.247, G.248, G.249, G.270, T.271 Ligands: ORO.6 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:S.24, C:S.24, C:A.49, C:N.104, C:N.104, C:K.170, C:K.170, C:N.197, C:S.221, C:G.222, C:G.248, C:G.249, C:G.270, C:T.271, C:T.271 Water bridges: C:S.24, C:K.48, C:V.250, C:V.250

2 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 13 residues within 4Å: Chain A: K.48, N.72, A.73, I.74, G.75, L.76, N.132, C.135, P.136, N.137, N.197, T.198 Ligands: FMN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.76 Hydrogen bonds: A:N.72, A:N.72, A:N.72, A:I.74, A:G.75, A:L.76, A:N.132, A:N.137, A:N.197, A:N.197 Salt bridges: A:K.48 ORO.6: 13 residues within 4Å: Chain C: K.48, N.72, A.73, I.74, G.75, L.76, N.132, C.135, P.136, N.137, N.197, T.198 Ligands: FMN.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.76 Hydrogen bonds: C:N.72, C:N.72, C:N.72, C:I.74, C:G.75, C:L.76, C:N.132, C:N.137, C:N.197, C:N.197, C:T.198 Salt bridges: C:K.48

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

FAD.3: 18 residues within 4Å: Chain A: E.65 Chain B: L.50, R.52, P.53, I.54, S.55, L.69, Y.70, R.71, T.77, G.78, T.79, I.119, E.220, S.221, R.222, M.223, P.252 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.53, B:E.220, B:P.252 Hydrogen bonds: B:R.52, B:P.53, B:S.55, B:L.69, B:R.71, B:T.77, B:G.78, B:T.79, B:T.79 Water bridges: B:R.222, B:M.223, B:M.223, A:E.65 Salt bridges: B:R.52, B:R.52 pi-Cation interactions: B:R.222 FAD.7: 18 residues within 4Å: Chain C: E.65 Chain D: L.50, R.52, P.53, I.54, S.55, L.69, Y.70, R.71, T.77, G.78, T.79, I.119, E.220, S.221, R.222, M.223, P.252 18 PLIP interactions: 1 interactions with chain C, 17 interactions with chain D Water bridges: C:E.65, D:R.222, D:M.223, D:M.223 Hydrophobic interactions: D:P.53, D:E.220, D:P.252 Hydrogen bonds: D:R.52, D:P.53, D:S.55, D:L.69, D:R.71, D:G.78, D:T.79, D:T.79 Salt bridges: D:R.52, D:R.52 pi-Cation interactions: D:R.222

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

FES.4: 12 residues within 4Å: Chain B: M.223, A.224, C.225, G.226, G.228, A.229, C.230, Y.231, A.232, C.233, K.246, C.248 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.225, B:C.230, B:C.233, B:C.248 FES.8: 12 residues within 4Å: Chain D: M.223, A.224, C.225, G.226, G.228, A.229, C.230, Y.231, A.232, C.233, K.246, C.248 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.225, D:C.230, D:C.233, D:C.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rowland, P. et al., Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster. Structure Fold.Des. (2000)

Release Date

2001-01-17

Peptides

DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT): AC
DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT): BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)

DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)

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