SMTL ID : 1wvg.1

Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.1: 26 residues within 4Å: Chain A: G.16, H.17, T.18, G.19, F.20, K.21, A.40, L.41, D.42, P.44, G.64, D.65, I.66, R.67, M.87, A.88, A.89, P.91, K.102, T.106, I.130, T.131, Y.157, K.161, R.206 Ligands: CXY.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:T.18, A:T.18, A:G.19, A:F.20, A:K.21, A:L.41, A:D.65, A:I.66, A:R.67, A:A.89, A:K.102, A:Y.157, A:Y.157, A:K.161, A:K.161 Water bridges: A:K.21, A:K.21, A:G.22, A:S.132, A:G.194, A:R.206, A:Y.242 Salt bridges: A:K.21, A:K.161, A:R.206, A:R.206 APR.3: 24 residues within 4Å: Chain B: G.16, H.17, T.18, G.19, F.20, K.21, A.40, L.41, D.42, P.44, G.64, D.65, I.66, R.67, M.87, A.88, A.89, P.91, T.106, I.130, T.131, Y.157, K.161, R.206 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:T.18, B:T.18, B:G.19, B:F.20, B:K.21, B:L.41, B:D.65, B:I.66, B:R.67, B:A.89, B:Y.157, B:K.161, B:R.206 Water bridges: B:K.21, B:G.22, B:T.131, B:S.132, B:Y.157 Salt bridges: B:K.21, B:K.161 APR.4: 26 residues within 4Å: Chain C: G.16, H.17, T.18, G.19, F.20, K.21, A.40, L.41, D.42, P.44, G.64, D.65, I.66, R.67, M.87, A.88, A.89, P.91, K.102, T.106, I.130, T.131, Y.157, K.161, R.206 Ligands: CXY.5 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:T.18, C:T.18, C:G.19, C:F.20, C:K.21, C:L.41, C:D.65, C:I.66, C:R.67, C:A.89, C:K.102, C:Y.157, C:K.161, C:K.161 Water bridges: C:K.21, C:K.21, C:G.22, C:S.132, C:G.194, C:R.206, C:Y.242 Salt bridges: C:K.21, C:K.161, C:R.206, C:R.206 APR.6: 24 residues within 4Å: Chain D: G.16, H.17, T.18, G.19, F.20, K.21, A.40, L.41, D.42, P.44, G.64, D.65, I.66, R.67, M.87, A.88, A.89, P.91, T.106, I.130, T.131, Y.157, K.161, R.206 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:T.18, D:T.18, D:T.18, D:G.19, D:F.20, D:K.21, D:L.41, D:D.65, D:I.66, D:R.67, D:A.89, D:Y.157, D:Y.157, D:K.161, D:R.206 Water bridges: D:K.21, D:G.22, D:T.131, D:S.132, D:Y.157 Salt bridges: D:K.21, D:K.161

2 x CXY: CYTIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE(Non-covalent)

CXY.2: 22 residues within 4Å: Chain A: P.91, L.92, V.93, S.132, D.133, K.134, Y.157, N.195, D.205, R.206, L.207, D.210, I.222, I.223, R.224, N.225, S.228, R.230, W.232, V.272, E.299 Ligands: APR.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:L.207 Hydrogen bonds: A:P.91, A:Y.157, A:N.195, A:R.206, A:R.206, A:L.207, A:D.210, A:D.210, A:R.224, A:N.225, A:N.225, A:S.228, A:E.299 Water bridges: A:D.133, A:V.196, A:V.196, A:I.208, A:R.224, A:R.224, A:R.224, A:R.230, A:R.230 Salt bridges: A:K.134, A:K.134, A:R.230 pi-Cation interactions: A:R.224 CXY.5: 22 residues within 4Å: Chain C: P.91, L.92, V.93, S.132, D.133, K.134, Y.157, N.195, D.205, R.206, L.207, D.210, I.222, I.223, R.224, N.225, S.228, R.230, W.232, V.272, E.299 Ligands: APR.4 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:L.207 Hydrogen bonds: C:P.91, C:Y.157, C:Y.157, C:N.195, C:R.206, C:R.206, C:L.207, C:D.210, C:R.224, C:N.225, C:N.225, C:S.228, C:E.299, C:E.299 Water bridges: C:D.133, C:V.196, C:V.196, C:I.208, C:R.224, C:R.224, C:R.224, C:R.230, C:R.230 Salt bridges: C:K.134, C:K.134, C:R.230 pi-Cation interactions: C:R.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koropatkin, N.M. et al., Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-01-26

Peptides

CDP-glucose 4,6-dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

CDP-glucose 4,6-dehydratase