SMTL ID : 7vfk.1

Crystal structure of SdgB (ligand-free form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: W.42, R.44, R.138, F.140, R.151 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.44, A:R.44, A:R.151, A:R.151 Water bridges: A:R.138 GOL.2: 8 residues within 4Å: Chain A: W.80, W.84, M.111, V.126, H.128, D.139, Y.141 Chain B: Q.197 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.84, A:D.139, A:Y.141, B:Q.197 Water bridges: B:Y.192 GOL.3: 5 residues within 4Å: Chain A: K.335, E.407, G.408, F.409, S.410 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.335, A:K.335, A:F.409, A:S.410 Water bridges: A:E.407, A:L.411 GOL.4: 7 residues within 4Å: Chain A: Q.197 Chain B: W.80, W.84, V.126, H.128, D.139, Y.141 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.84, B:D.139, B:Y.141, A:Q.197, A:Q.197 GOL.5: 6 residues within 4Å: Chain B: W.42, R.151, E.162, F.164, K.175, E.203 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.151, B:K.175, B:K.175 Water bridges: B:W.42, B:E.203

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 9 residues within 4Å: Chain A: K.137, F.163, Y.165, T.171 Chain B: F.163, Y.165, T.171, E.174, Y.192 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.165, B:Y.165, B:T.171 Water bridges: B:Y.192, A:Y.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, D.G. et al., Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins. Acta Crystallogr D Struct Biol (2021)

Release Date

2021-11-24

Peptides

Glycosyl transferase, group 1 family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycosyl transferase, group 1 family protein

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