SMTL ID : 8v4g.1

X-ray structure of the NADP-dependent reductase from Campylobacter jejuni responsible for the synthesis of CDP-glucitol in the presence of CDP and NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 23 residues within 4Å: Chain A: G.34, N.36, G.37, Y.38, I.39, R.58, K.62, C.96, A.97, A.98, P.99, T.100, I.115, N.119, L.138, S.139, Y.169, K.173, L.196, T.197, Q.198, A.199, R.210 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:L.196 Hydrogen bonds: A:G.34, A:N.36, A:N.36, A:Y.38, A:I.39, A:R.58, A:C.96, A:A.98, A:T.100, A:N.119, A:K.173, A:Q.198, A:A.199, A:R.210 Water bridges: A:N.36, A:N.36, A:G.37, A:G.40, A:R.58, A:R.58, A:R.58, A:R.58, A:R.58, A:N.59, A:K.62, A:K.62 Salt bridges: A:R.58, A:K.62 pi-Cation interactions: A:R.58, A:R.58 NAP.6: 25 residues within 4Å: Chain B: G.34, A.35, N.36, G.37, Y.38, I.39, R.58, K.62, C.96, A.97, A.98, P.99, T.100, I.115, N.119, L.138, S.139, T.140, Y.169, K.173, L.196, T.197, Q.198, A.199, R.210 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:L.196 Hydrogen bonds: B:G.34, B:N.36, B:N.36, B:G.37, B:Y.38, B:I.39, B:G.40, B:C.96, B:A.98, B:N.119, B:K.173, B:Q.198, B:A.199, B:R.210 Water bridges: B:G.34, B:N.36, B:R.58, B:R.58, B:R.58, B:K.62, B:K.62, B:K.62, B:K.62, B:T.100, B:R.210 Salt bridges: B:R.58, B:K.62, B:R.210, B:R.210 pi-Cation interactions: B:R.58

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.2: 7 residues within 4Å: Chain A: V.211, T.226, L.227, F.228, T.229, R.235, I.271 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.226, A:F.228, A:T.229, A:T.229 Water bridges: A:G.231 CDP.7: 13 residues within 4Å: Chain B: S.102, R.166, V.211, D.214, F.215, T.226, L.227, F.228, T.229, R.235, I.271, Y.297, L.298 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.211 Hydrogen bonds: B:S.102, B:S.102, B:V.211, B:D.214, B:F.228, B:T.229, B:R.235, B:Y.297, B:L.298 Water bridges: B:S.102, B:R.166, B:G.231, B:R.235 Salt bridges: B:R.166, B:R.235, B:R.235

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: E.81, D.82 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: K.186 Chain B: N.108, P.109, I.110, D.111 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: L.56, H.95, A.97, N.119, N.122, I.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.119, A:N.122 EDO.5: 5 residues within 4Å: Chain A: S.279, A.280, N.283, V.284, Q.285 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.279, A:Q.285 Water bridges: A:N.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, M.K. et al., Biosynthesis of Cytidine Diphosphate-6-d-Glucitol for the Capsular Polysaccharides of Campylobacter jejuni. Biochemistry (2024)

Release Date

2023-12-20

Peptides

Putative nucleotide sugar dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative nucleotide sugar dehydratase