SMTL ID : 7pvi.1

dTDP-sugar epimerase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

2 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.1: 3 residues within 4Å: Chain A: P.40, K.41, V.42 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.41, A:V.42 Water bridges: A:N.131, A:H.133 Salt bridges: A:K.41 XYP.6: 9 residues within 4Å: Chain A: F.50 Chain B: N.72, H.86, Q.94, K.96, Y.162, E.167 Ligands: FLC.8, NA.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.72, B:H.86, B:Q.94, B:K.96, B:K.96, B:E.167 Water bridges: B:E.167 Salt bridges: B:K.96

2 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.2: 5 residues within 4Å: Chain A: F.119, G.120, K.121, D.176, L.199 No protein-ligand interaction detected (PLIP) XYS.7: 5 residues within 4Å: Chain B: F.119, G.120, K.121, D.176, L.199 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.121, B:K.121

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

NA.3: 3 residues within 4Å: Chain A: F.49, S.129, N.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.132, A:N.132 NA.4: 4 residues within 4Å: Chain A: D.71, N.72, L.155, Y.156 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.72, A:N.72, A:Y.156 Water bridges: B:T.53 NA.5: 2 residues within 4Å: Chain A: E.67, T.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.67, A:E.67 Water bridges: A:E.67 NA.9: 4 residues within 4Å: Chain B: G.63, I.64, N.65, W.136 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.63, B:N.65, B:N.65 NA.10: 1 residues within 4Å: Chain B: K.157 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:D.71, B:D.71, A:T.53, A:D.71 NA.11: 5 residues within 4Å: Chain B: Y.87, Q.88, Q.94, E.167 Ligands: XYP.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.94, B:K.96

1 x FLC: CITRATE ANION(Non-covalent)

FLC.8: 10 residues within 4Å: Chain A: R.47, F.50 Chain B: S.74, R.83, H.86, K.96, H.143, M.145, Y.156 Ligands: XYP.6 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.83 Hydrogen bonds: B:S.74, B:Y.156, B:Y.156 Water bridges: B:K.96, B:K.96, B:H.143, A:R.47 Salt bridges: B:R.83, B:R.83, B:H.86, B:H.86, B:K.96, B:H.143, A:R.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cross, A.R. et al., Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases. J.Biol.Chem. (2022)

Release Date

2022-04-20

Peptides

dTDP-4-dehydrorhamnose 3,5-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

dTDP-4-dehydrorhamnose 3,5-epimerase

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