SMTL ID : 5bjy.1

x-ray structure of the PglF 4,5-dehydratase from campylobacter jejuni, variant M405Y, in complex with UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 15 residues within 4Å: Chain A: K.154, N.190, S.197, V.198, K.201, F.202, T.213, L.214, T.215, I.219, R.221, I.256, R.280, E.283 Ligands: EDO.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.198 Hydrogen bonds: A:N.190, A:V.198, A:K.201, A:T.213, A:T.213, A:T.215, A:R.280 Water bridges: A:R.221, A:E.283 Salt bridges: A:K.154, A:R.221 UDP.9: 14 residues within 4Å: Chain B: K.154, N.190, S.197, V.198, K.201, T.213, L.214, T.215, I.219, R.221, I.256, R.280, E.283 Ligands: EDO.12 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.198 Hydrogen bonds: B:N.190, B:V.198, B:K.201, B:T.213, B:T.213, B:T.215, B:R.280 Water bridges: B:R.221, B:R.221, B:E.283 Salt bridges: B:K.154, B:R.221

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

NAD.2: 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, Y.162, K.166, F.188, G.189, N.190, V.191, S.194, S.195 Ligands: EDO.4 31 PLIP interactions: 30 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.40, A:F.188 Hydrogen bonds: A:G.37, 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:H.61, A:S.62, A:S.62, A:S.195, B:Y.64 Salt bridges: A:K.112, A:K.112 pi-Stacking: A:H.61, A:H.61 NAD.10: 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, Y.162, K.166, F.188, G.189, N.190, V.191, S.194, S.195 Ligands: EDO.12 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:F.188 Hydrogen bonds: B:G.37, 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:V.191, B:S.194, B:S.194, B:S.195 Water bridges: B:G.38, B:G.41, B:H.61, B:S.62, B:S.62, B:A.109, B:I.150, B:S.195 Salt bridges: B:K.112, B:K.112 pi-Stacking: B:H.61, B:H.61

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

EDO.3: 5 residues within 4Å: Chain A: G.37, G.38, T.39, S.42 Ligands: NA.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.42, A:S.42 Water bridges: A:S.195, A:S.195, A:S.195 EDO.4: 8 residues within 4Å: Chain A: K.112, H.113, S.194, S.195, G.196, S.197 Ligands: UDP.1, NAD.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.194, A:S.194 Water bridges: A:K.112 EDO.5: 3 residues within 4Å: Chain A: V.311, D.312, W.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.312 EDO.11: 5 residues within 4Å: Chain B: G.37, G.38, T.39, S.42 Ligands: NA.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.42, B:S.42 Water bridges: B:S.195 EDO.12: 8 residues within 4Å: Chain B: K.112, H.113, S.194, S.195, G.196, S.197 Ligands: UDP.9, NAD.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.194, B:S.194 Water bridges: B:K.112, B:V.114

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

NA.6: 2 residues within 4Å: Chain A: D.18, S.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.18, A:S.20 NA.7: 2 residues within 4Å: Chain A: K.77, I.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.77 NA.8: 2 residues within 4Å: Chain A: K.46 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.46, A:K.46 Water bridges: A:S.42 NA.13: 2 residues within 4Å: Chain B: D.18, S.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.18, B:S.20 NA.14: 2 residues within 4Å: Chain B: K.46 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.46, B:K.46 Water bridges: B:S.42 NA.15: 2 residues within 4Å: Chain B: K.77, I.80 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.80, B:I.80

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