SMTL ID : 5bjv.1

X-ray structure of the PglF UDP-N-acetylglucosamine 4,6-dehydratase from Campylobacterjejuni, D396N/K397A variant in complex with UDP-N-acrtylglucosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: G.35, G.37, G.38, T.39, I.40, D.60, H.61, S.62, N.65, L.85, S.86, I.87, A.108, A.109, A.110, K.112, N.127, I.150, S.151, T.152, K.166, F.188, G.189, N.190, V.191, S.194, S.195 Ligands: UD1.2 28 PLIP interactions: 27 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.40, A:F.188 Hydrogen bonds: A:T.39, A:T.39, A:I.40, A:H.61, A:S.62, A:N.65, A:I.87, A:A.108, A:A.110, A:K.112, A:N.127, A:N.127, A:K.166, A:V.191, A:S.194, A:S.194, A:S.195 Water bridges: A:G.38, A:G.41, A:S.86, A:S.195, B:Y.64 Salt bridges: A:K.112, A:K.112 pi-Stacking: A:H.61, A:H.61 NAD.7: 28 residues within 4Å: Chain B: G.35, G.37, G.38, T.39, I.40, D.60, H.61, S.62, N.65, L.85, S.86, I.87, A.108, A.109, A.110, K.112, N.127, I.150, S.151, T.152, K.166, F.188, G.189, N.190, V.191, S.194, S.195 Ligands: UD1.8 32 PLIP interactions: 30 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.40, B:F.188 Hydrogen bonds: B:G.37, B:T.39, B:T.39, B:I.40, B:H.61, B:S.62, B:N.65, B:I.87, B:A.110, B:K.112, B:N.127, B:N.127, B:K.166, B:K.166, B:V.191, B:S.194, B:S.194, B:S.195 Water bridges: B:G.38, B:G.41, B:S.62, B:S.62, B:S.86, B:S.195, A:E.63, A:E.63 Salt bridges: B:K.112, B:K.112 pi-Stacking: B:H.61, B:H.61

2 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.2: 21 residues within 4Å: Chain A: K.112, H.113, T.152, A.154, M.162, G.189, N.190, S.194, G.196, S.197, V.198, K.201, T.213, L.214, T.215, I.219, R.221, I.256, R.280, E.283 Ligands: NAD.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.198 Hydrogen bonds: A:K.112, A:K.112, A:N.190, A:S.194, A:V.198, A:T.213, A:T.213, A:T.215, A:R.280 Water bridges: A:T.152, A:N.153, A:R.221, A:R.221, A:R.221, A:R.280, A:R.280 Salt bridges: A:R.221, A:R.280, A:R.280 UD1.8: 21 residues within 4Å: Chain B: K.112, H.113, T.152, A.154, M.162, G.189, N.190, S.194, G.196, S.197, V.198, K.201, T.213, L.214, T.215, I.219, R.221, I.256, R.280, E.283 Ligands: NAD.7 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:K.112, B:V.198 Hydrogen bonds: B:K.112, B:K.112, B:T.152, B:N.190, B:N.190, B:V.198, B:T.213, B:T.215, B:T.215, B:R.280 Water bridges: B:T.152, B:N.153, B:N.190, B:R.221, B:R.221, B:Y.222, B:R.280, B:R.280, B:E.283, B:E.283 Salt bridges: B:R.221, B:R.280, B:R.280

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

EDO.3: 6 residues within 4Å: Chain A: N.120, P.121, H.122, S.123 Chain B: I.83, L.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.122, A:S.123 EDO.4: 3 residues within 4Å: Chain A: G.37, G.38, T.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.37 Water bridges: A:S.195 EDO.9: 6 residues within 4Å: Chain A: I.83, L.84 Chain B: N.120, P.121, H.122, S.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.122, B:S.123

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: K.77, I.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.77 NA.6: 1 residues within 4Å: Chain A: K.46 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.46 Water bridges: A:S.42, A:K.68, A:K.68, A:K.68, A:D.72, A:D.72 NA.10: 2 residues within 4Å: Chain B: K.77, I.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.80 NA.11: 1 residues within 4Å: Chain B: K.46 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.46, B:K.46 Water bridges: B:S.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riegert, A.S. et al., Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily. Biochemistry (2017)

Release Date

2017-11-08

Peptides

WlaL protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

WlaL protein