SMTL ID : 7x32.3 (3 other biounits)

Crystal structure of E. coli NfsB in complex with berberine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: R.10, H.11, S.12, K.14, N.71, K.74, Y.144, P.163, I.164, E.165, G.166, N.200, K.205, R.207 Chain B: P.38, S.39, S.40, T.41, N.42, Q.142, L.145 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.144, A:P.163, B:L.145 Hydrogen bonds: A:S.12, A:S.12, A:S.12, A:K.14, A:N.71, A:N.71, A:K.74, A:E.165, A:G.166, A:N.200, B:S.39, B:T.41 Water bridges: A:N.200, A:K.205, A:R.207, A:R.207, B:R.107 Salt bridges: A:R.10, A:K.205, A:R.207 FMN.5: 22 residues within 4Å: Chain A: P.38, S.39, S.40, T.41, N.42, Q.142, L.145 Chain B: R.10, H.11, S.12, K.14, F.70, N.71, K.74, V.162, P.163, I.164, E.165, N.200, K.205, R.207 Ligands: BER.2 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:K.14, B:F.70, B:V.162 Hydrogen bonds: B:S.12, B:S.12, B:S.12, B:E.165, B:N.200, A:S.39, A:T.41, A:N.42 Water bridges: B:K.205, B:K.205, B:R.207, B:R.207 Salt bridges: B:R.10, B:K.205, B:R.207

1 x BER: BERBERINE(Non-covalent)

BER.2: 15 residues within 4Å: Chain A: S.40, T.41, N.42, E.102, R.107, F.108, N.117, R.121, F.124 Chain B: K.14, F.70, E.165, G.166, N.200 Ligands: FMN.5 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.70, A:T.41, A:N.42, A:F.124 Hydrogen bonds: B:G.166, A:T.41, A:R.107, A:N.117 Water bridges: B:N.200

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: D.2 Chain B: D.2, I.3, V.6, A.156 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.2, A:D.2 Water bridges: A:D.2

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 3 residues within 4Å: Chain A: L.8, K.205 Chain B: Y.36 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wen, H.Y. et al., Structural basis for the transformation of the traditional medicine berberine by bacterial nitroreductase. Acta Crystallogr D Struct Biol (2022)

Release Date

2022-10-12

Peptides

Dihydropteridine reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

Dihydropteridine reductase

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