SMTL ID : 7pwb.1

dTDP-sugar epimerase from Coxiella burnetii in complex with dTDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

4 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.1: 12 residues within 4Å: Chain A: Q.70, N.72, R.83, H.86, Y.162, E.167, K.192 Chain B: F.43, R.47, F.50, E.52 Ligands: CIT.3 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.162, B:F.50 Hydrogen bonds: A:Q.70, A:N.72, A:Y.169, B:E.52 Water bridges: A:K.96, A:E.167, A:K.192, A:K.192, A:K.192, B:R.47 Salt bridges: A:R.83, A:H.86, A:K.192, B:R.47, B:R.47 pi-Stacking: A:Y.162, B:F.50 TYD.2: 5 residues within 4Å: Chain A: K.121, W.122, I.177, N.178, K.180 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.122, A:W.122, A:N.178 Salt bridges: A:K.180 pi-Stacking: A:W.122 TYD.7: 12 residues within 4Å: Chain A: F.43, R.47, F.50, E.52 Chain B: Q.70, N.72, R.83, H.86, Y.162, E.167, K.192 Ligands: CIT.9 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.50, B:Y.162 Hydrogen bonds: A:E.52, A:E.52, B:Q.70, B:N.72, B:Y.169, B:Y.169 Water bridges: A:R.47, A:R.47, B:K.192 Salt bridges: A:R.47, A:R.47, B:R.83, B:H.86, B:K.192 pi-Stacking: A:F.50, B:Y.162 TYD.8: 5 residues within 4Å: Chain B: K.121, W.122, I.177, N.178, K.180 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.122, B:W.122, B:N.178 Water bridges: B:D.176 Salt bridges: B:K.180 pi-Stacking: B:W.122, B:W.122

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 12 residues within 4Å: Chain A: S.74, R.83, G.84, H.86, K.96, H.143, G.144, M.145, L.154, Y.156 Chain B: F.50 Ligands: TYD.1 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.83, A:Y.156, B:F.50 Hydrogen bonds: A:S.74, A:H.86 Water bridges: A:K.96, A:K.96, A:K.96 Salt bridges: A:R.83, A:H.86, A:H.86, A:K.96, A:H.143, A:H.143 CIT.9: 12 residues within 4Å: Chain A: F.50 Chain B: S.74, R.83, G.84, H.86, K.96, H.143, G.144, M.145, L.154, Y.156 Ligands: TYD.7 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.83, B:Y.156, A:F.50 Hydrogen bonds: B:S.74, B:H.86, B:H.143 Water bridges: B:K.96 Salt bridges: B:R.83, B:H.86, B:H.86, B:K.96, B:H.143, B:H.143

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

EDO.4: 3 residues within 4Å: Chain A: E.126, N.131, H.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.126, A:E.126, A:N.131, A:H.133 EDO.5: 5 residues within 4Å: Chain A: R.168, Y.169, V.197, A.202, E.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.169, A:E.203, A:E.203 EDO.6: 4 residues within 4Å: Chain A: R.113, P.139, Q.207, H.209 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.113, A:P.139, A:H.209 Water bridges: A:Q.207 EDO.10: 6 residues within 4Å: Chain B: Y.169, K.192, A.195, G.196, V.197 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.192, B:V.197 EDO.11: 4 residues within 4Å: Chain B: R.113, P.139, Q.207, H.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.113, B:Q.207, B:H.209 EDO.12: 7 residues within 4Å: Chain B: Y.87, R.168, Y.169, V.197, A.202, E.203 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.169, B:E.203 EDO.13: 6 residues within 4Å: Chain B: P.24, F.25, F.27, D.58, R.61, H.62 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.24, B:F.25, B:R.61, B:H.62

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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