SMTL ID : 7x32.1 (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

FMN.1: 24 residues within 4Å: Chain A: R.10, H.11, S.12, K.14, F.70, N.71, K.74, Y.144, V.162, 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 Ligands: BER.4 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.144, A:P.163 Hydrogen bonds: A:S.12, A:S.12, A:S.12, A:K.14, 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, B:N.42 Water bridges: A:K.205, A:R.207, A:R.207, B:R.107 Salt bridges: A:R.10, A:K.205, A:R.207 FMN.3: 21 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, P.163, I.164, E.165, G.166, N.200, K.205, R.207 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:S.39, A:T.41, A:N.42, A:Q.142, B:S.12, B:S.12, B:S.12, B:S.12, B:E.165, B:N.200 Water bridges: A:R.107, B:K.14, B:K.205, B:R.207, B:R.207 Hydrophobic interactions: B:F.70 Salt bridges: B:R.10, B:K.205, B:R.207

1 x GOL: GLYCEROL

GOL.2: 5 residues within 4Å: Chain A: D.2, I.4, S.5 Chain B: E.25, Q.29 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.2, A:S.5, B:E.25, B:Q.29

1 x BER: BERBERINE

BER.4: 14 residues within 4Å: Chain A: K.14, F.70, F.199, L.203 Chain B: S.40, T.41, E.102, R.107, F.108, N.117, R.121, F.124 Ligands: FMN.1, DMS.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.41, B:R.107, B:N.117

1 x DMS: DIMETHYL SULFOXIDE

DMS.5: 4 residues within 4Å: Chain B: N.117, G.120, R.121 Ligands: BER.4 No protein-ligand interaction detected (PLIP)

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
A

B
C

Dihydropteridine reductase

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