SMTL ID : 6ds1.1

Crystal structure of Cj0485 dehydrogenase in complex with NADP+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 28 residues within 4Å: Chain A: G.14, K.17, G.18, I.19, S.38, R.39, S.40, I.61, D.62, L.63, K.64, N.89, A.90, G.91, N.112, Y.117, I.138, V.139, S.140, Y.153, K.157, P.183, A.184, E.185, V.186, T.188, L.190, Y.191 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:P.183 Hydrogen bonds: A:G.14, A:K.17, A:I.19, A:S.38, A:R.39, A:R.39, A:R.39, A:L.63, A:K.64, A:N.89, A:N.112, A:K.157, A:V.186, A:V.186 Water bridges: A:K.17, A:G.20, A:S.40, A:S.40, A:N.89, A:T.92, A:T.188 Salt bridges: A:K.17, A:R.39 pi-Cation interactions: A:R.39, A:R.39 NAP.4: 28 residues within 4Å: Chain B: G.14, K.17, G.18, I.19, S.38, R.39, S.40, I.61, D.62, L.63, K.64, N.89, A.90, G.91, N.112, Y.117, I.138, V.139, S.140, Y.153, K.157, P.183, A.184, E.185, V.186, T.188, L.190, Y.191 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:P.183 Hydrogen bonds: B:G.14, B:K.17, B:I.19, B:S.38, B:R.39, B:R.39, B:R.39, B:D.62, B:L.63, B:K.64, B:N.89, B:N.112, B:V.186, B:V.186, B:T.188 Water bridges: B:K.17, B:G.18, B:G.20, B:S.40, B:S.40, B:N.89 Salt bridges: B:K.17, B:R.39 pi-Cation interactions: B:R.39, B:R.39 NAP.6: 28 residues within 4Å: Chain C: G.14, K.17, G.18, I.19, S.38, R.39, S.40, I.61, D.62, L.63, K.64, N.89, A.90, G.91, N.112, Y.117, I.138, V.139, S.140, Y.153, K.157, P.183, A.184, E.185, V.186, T.188, L.190, Y.191 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:P.183 Hydrogen bonds: C:G.14, C:K.17, C:I.19, C:S.38, C:R.39, C:R.39, C:R.39, C:L.63, C:K.64, C:N.89, C:N.112, C:Y.117, C:Y.153, C:V.186, C:V.186 Water bridges: C:K.17, C:K.17, C:G.20, C:S.40, C:S.40, C:N.89, C:T.92 Salt bridges: C:K.17, C:R.39 pi-Cation interactions: C:R.39, C:R.39 NAP.8: 28 residues within 4Å: Chain D: G.14, K.17, G.18, I.19, S.38, R.39, S.40, I.61, D.62, L.63, K.64, N.89, A.90, G.91, N.112, Y.117, I.138, V.139, S.140, Y.153, K.157, P.183, A.184, E.185, V.186, T.188, L.190, Y.191 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:P.183 Hydrogen bonds: D:G.14, D:K.17, D:I.19, D:S.38, D:R.39, D:R.39, D:R.39, D:D.62, D:L.63, D:K.64, D:N.89, D:N.112, D:Y.117, D:Y.153, D:V.186, D:V.186 Water bridges: D:G.20, D:S.40, D:N.89, D:K.157, D:T.188, D:Y.191 Salt bridges: D:K.17, D:R.39 pi-Cation interactions: D:R.39, D:R.39

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: N.7, K.8, V.9, H.80, G.81, G.82, I.83, Y.84, E.131 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.9, A:G.81, A:Y.84, A:E.131 Water bridges: A:E.131 GOL.9: 5 residues within 4Å: Chain A: E.99 Chain D: E.70, K.74, K.122, E.123 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.70, D:K.74, D:K.74, D:K.122 Water bridges: A:E.99 GOL.10: 9 residues within 4Å: Chain D: N.7, K.8, V.9, H.80, G.81, G.82, I.83, Y.84, E.131 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.9, D:Y.84, D:E.131

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: I.61, D.62, N.65 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: I.61, D.62, N.65 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: I.61, D.62, N.65 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain D: I.61, D.62, N.65 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garber, J.M. et al., The gastrointestinal pathogen Campylobacter jejuni metabolizes sugars with potential help from commensal Bacteroides vulgatus. Commun Biol (2020)

Release Date

2019-07-10

Peptides

Putative oxidoreductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative oxidoreductase

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