SMTL ID : 5m63.1 (1 other biounit)

Crystal structure of group B Streptococcus type III DP2 oligosaccharide bound to Fab NVS-1-19-5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.1: 10 residues within 4Å: Chain A: F.51, R.70, F.125, Y.126, H.127 Chain B: Y.52, R.56, Y.115 Ligands: BGC-GAL-NAG-GAL-SIA-BGC-GAL.2, 7GW.6 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.52 Hydrogen bonds: B:R.56, A:H.127 Water bridges: A:R.70, A:R.70 Salt bridges: A:R.70

1 x BGC- GAL- NAG- GAL- SIA- BGC- GAL: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[beta-D-galactopyranose-(1-4)-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-NAG-GAL-SIA-BGC-GAL.2: 13 residues within 4Å: Chain A: E.121, V.124, Y.126 Chain B: N.53, N.54, N.55, R.56, K.74, A.75, S.76, A.91 Ligands: GAL-SIA.1, 7GW.6 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.54, B:N.53, B:N.55, B:R.56, B:R.56, B:K.74, A:E.121 Hydrophobic interactions: A:Y.126

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

EDO.3: 4 residues within 4Å: Chain A: E.64, W.65 Chain B: A.124, F.125 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.125, A:W.65 EDO.4: 2 residues within 4Å: Chain A: A.34, S.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.35, A:S.35 EDO.5: 1 residues within 4Å: Chain A: V.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.152 EDO.7: 3 residues within 4Å: Chain B: Y.111, G.127, G.128 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.31, B:Y.111, A:K.61 EDO.8: 2 residues within 4Å: Chain B: Q.62, A.64 No protein-ligand interaction detected (PLIP) EDO.9: 2 residues within 4Å: Chain B: Q.61, L.71 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain B: Q.66, P.67 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.66

1 x 7GW: (2~{R},3~{R},4~{S},5~{S})-2-[bis(oxidanyl)methyl]-5-(hydroxymethyl)oxolane-3,4-diol(Non-functional Binders)

7GW.6: 2 residues within 4Å: Ligands: GAL-SIA.1, BGC-GAL-NAG-GAL-SIA-BGC-GAL.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carboni, F. et al., Structure of a protective epitope of group B Streptococcus type III capsular polysaccharide. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-05-03

Peptides

H chain of Fab NVS-1-19-5: A
L chain of Fab NVS-1-19-5: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

H chain of Fab NVS-1-19-5

L chain of Fab NVS-1-19-5

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