SMTL ID : 8zax.1

Crystal structure of a short-chain dehydrogenase from Lactobacillus fermentum with NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 26 residues within 4Å: Chain A: G.13, T.15, K.16, G.17, I.18, G.38, R.39, H.40, Q.60, D.61, V.62, N.88, A.89, G.90, I.91, I.111, I.137, S.138, S.139, Y.152, K.156, P.184, G.185, V.186, I.187, T.189 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.18, A:P.184 Hydrogen bonds: A:G.13, A:T.15, A:I.18, A:R.39, A:D.61, A:V.62, A:N.88, A:G.90, A:Y.152, A:K.156, A:G.185, A:I.187 Water bridges: A:K.16, A:K.16, A:G.19, A:G.19, A:H.40, A:H.40, A:H.40, A:T.189, A:T.189 Salt bridges: A:K.16, A:H.40 NAP.2: 27 residues within 4Å: Chain B: G.13, G.14, T.15, K.16, G.17, I.18, T.37, G.38, R.39, H.40, Q.60, D.61, V.62, N.88, A.89, G.90, I.111, I.137, S.138, S.139, Y.152, K.156, P.184, G.185, V.186, I.187, T.189 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.18, B:P.184 Hydrogen bonds: B:G.13, B:G.13, B:T.15, B:T.15, B:K.16, B:I.18, B:R.39, B:R.39, B:H.40, B:D.61, B:V.62, B:N.88, B:G.90, B:Y.152, B:K.156, B:G.185, B:I.187 Water bridges: B:G.19, B:G.19, B:T.189 Salt bridges: B:K.16, B:R.39 NAP.3: 26 residues within 4Å: Chain C: G.13, T.15, K.16, G.17, I.18, G.38, R.39, H.40, Q.60, D.61, V.62, N.88, A.89, G.90, I.91, I.111, I.137, S.138, S.139, Y.152, K.156, P.184, G.185, V.186, I.187, T.189 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:I.18, C:P.184 Hydrogen bonds: C:G.13, C:T.15, C:T.15, C:I.18, C:R.39, C:D.61, C:D.61, C:V.62, C:N.88, C:G.90, C:K.156, C:G.185, C:I.187, C:T.189 Water bridges: C:K.16, C:K.16, C:G.19, C:G.19, C:H.40, C:E.43, C:T.189 Salt bridges: C:K.16, C:H.40 NAP.4: 27 residues within 4Å: Chain D: G.13, G.14, T.15, K.16, G.17, I.18, T.37, G.38, R.39, H.40, Q.60, D.61, V.62, N.88, A.89, G.90, I.111, I.137, S.138, S.139, Y.152, K.156, P.184, G.185, V.186, I.187, T.189 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:I.18, D:P.184 Hydrogen bonds: D:G.13, D:G.13, D:T.15, D:T.15, D:T.15, D:K.16, D:I.18, D:R.39, D:R.39, D:H.40, D:D.61, D:D.61, D:V.62, D:N.88, D:G.90, D:K.156, D:G.185, D:I.187, D:T.189 Water bridges: D:G.19, D:G.19 Salt bridges: D:K.16, D:R.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., Structure-Guided Engineering of a Short-Chain Dehydrogenase LfSDR1 for Efficient Biosynthesis of (R)-9-(2-Hydroxypropyl)adenine, the Key Intermediate of Tenofovir. Adv.Synth.Catal. (2024)

Release Date

2024-10-30

Peptides

SDR family oxidoreductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

SDR family oxidoreductase

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