SMTL ID : 7ec3.1

Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycosylated peptide)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x SER- ASP- SER- ASP- SER- ASP- SER- ASP: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE(Non-covalent)

SER-ASP-SER-ASP-SER-ASP-SER-ASP.1: 12 residues within 4Å: Chain A: R.102, F.109, Y.112, Y.125, N.127, F.129, R.133, K.135, R.138, Q.157 Ligands: NAG.7, NAG.8 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.112 Hydrogen bonds: A:R.102, A:Y.112, A:Y.125, A:Y.125, A:Y.125, A:N.127, A:N.127, A:K.135, A:Q.157 Water bridges: A:R.102 Salt bridges: A:R.102, A:R.133, A:K.135, A:R.138 SER-ASP-SER-ASP-SER-ASP-SER-ASP.2: 11 residues within 4Å: Chain B: R.102, F.109, Y.112, Y.125, N.127, F.129, R.133, K.135, R.138, Q.157 Ligands: NAG.9 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.112 Hydrogen bonds: B:R.102, B:Y.112, B:Y.125, B:Y.125, B:N.127, B:R.133, B:K.135, B:Q.157 Salt bridges: B:R.102, B:R.133, B:K.135, B:R.138

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.3: 18 residues within 4Å: Chain A: L.14, G.16, K.19, V.328, R.330, K.335, Y.359, G.360, G.385, F.386, L.387, L.390, E.407, S.410, L.411, A.412, E.415 Ligands: NAG.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.19, A:L.387, A:L.387, A:L.411, A:A.412, A:E.415, A:E.415 Water bridges: A:R.330, A:K.335 Salt bridges: A:R.330, A:K.335, A:K.335 pi-Stacking: A:F.386 UDP.5: 17 residues within 4Å: Chain B: L.14, G.16, K.19, V.328, R.330, K.335, Y.359, G.385, F.386, L.387, L.390, E.407, S.410, L.411, A.412, E.415 Ligands: NAG.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.328 Hydrogen bonds: B:G.16, B:L.387, B:L.387, B:L.411, B:A.412, B:E.415 Salt bridges: B:R.330, B:K.335, B:K.335 pi-Stacking: B:F.386

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.4: 12 residues within 4Å: Chain A: A.20, H.247, S.248, V.305, E.334, M.406, E.407, G.408, F.409, S.410, L.411 Ligands: UDP.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.247, A:K.335, A:E.407, A:G.408, A:F.409, A:S.410, A:L.411 NAG.6: 14 residues within 4Å: Chain B: G.16, I.17, A.20, H.247, S.248, V.305, E.334, M.406, E.407, G.408, F.409, S.410, L.411 Ligands: UDP.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.247, B:E.334, B:E.407, B:E.407, B:G.408, B:F.409, B:S.410, B:L.411 NAG.7: 5 residues within 4Å: Chain A: R.102, Y.104, R.133 Ligands: SER-ASP-SER-ASP-SER-ASP-SER-ASP.1, SER-ASP-SER-ASP-SER-ASP-SER-ASP.1 No protein-ligand interaction detected (PLIP) NAG.8: 6 residues within 4Å: Chain A: S.98, D.100, Y.112 Ligands: SER-ASP-SER-ASP-SER-ASP-SER-ASP.1, SER-ASP-SER-ASP-SER-ASP-SER-ASP.1, SER-ASP-SER-ASP-SER-ASP-SER-ASP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.100, A:Y.112 NAG.9: 5 residues within 4Å: Chain B: D.100, Y.112 Ligands: SER-ASP-SER-ASP-SER-ASP.2, SER-ASP-SER-ASP-SER-ASP.2, SER-ASP-SER-ASP-SER-ASP.2 No protein-ligand interaction detected (PLIP)

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

2022-03-16

Peptides

Glycosyl transferase, group 1 family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Glycosyl transferase, group 1 family protein

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