SMTL ID : 7vfo.1

Crystal structure of SdgB (Phosphate-binding form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

11 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: T.14, G.15, R.329, K.334 Ligands: PO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.15 Salt bridges: A:R.329, A:K.334 PO4.2: 8 residues within 4Å: Chain A: I.16, D.223, R.224, N.225, V.244, H.246, V.264, Y.265 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.223, A:R.224, A:N.225, A:N.225, A:H.246 Salt bridges: A:H.246 PO4.3: 3 residues within 4Å: Chain A: N.7, R.224, Y.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.7, A:Y.227 Salt bridges: A:R.224 PO4.4: 8 residues within 4Å: Chain A: G.15, K.18, E.406, F.408, S.409, L.410, A.411 Ligands: PO4.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.406, A:F.408, A:L.410, A:A.411 Salt bridges: A:K.18, A:K.334 PO4.5: 4 residues within 4Å: Chain A: W.41, R.43, R.150 Ligands: PO4.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.43, A:R.150 PO4.6: 4 residues within 4Å: Chain A: Y.111, N.126, F.128, K.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.126 Salt bridges: A:K.134 PO4.7: 2 residues within 4Å: Chain A: R.137 Ligands: PO4.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.137 PO4.8: 4 residues within 4Å: Chain B: G.15, R.329, K.334 Ligands: PO4.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.15 Salt bridges: B:R.329, B:K.334 PO4.9: 3 residues within 4Å: Chain B: N.7, R.224, Y.227 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.7 Salt bridges: B:R.224 PO4.10: 9 residues within 4Å: Chain B: G.15, K.18, K.334, E.406, F.408, S.409, L.410, A.411 Ligands: PO4.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.409, B:L.410, B:A.411 Salt bridges: B:K.18, B:K.334 PO4.11: 4 residues within 4Å: Chain B: Y.111, N.126, F.128, K.134 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.126 Salt bridges: B:K.134

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
B

B
A

Glycosyl transferase, group 1 family protein

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