SMTL ID : 6vu6.1 (1 other biounit)

Sialic acid binding region of Streptococcus Sanguinis SK1 adhesin bound to 3'sLn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

NAG-GAL-SIA.1: 13 residues within 4Å: Chain A: N.42, I.43, E.44, D.53, G.93, D.94, R.95, Y.96, T.97, K.98, Y.99, D.114, K.115 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.99, A:Y.99, A:N.42, A:D.53, A:R.95, A:T.97, A:T.97, A:K.98 Hydrophobic interactions: A:D.114, A:Y.96 Water bridges: A:E.44, A:E.44, A:K.115 NAG-GAL-SIA.2: 8 residues within 4Å: Chain A: A.245, S.248, T.249, T.252, G.294, K.296, Y.297, T.298 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.248, A:K.296, A:T.298 Water bridges: A:T.249 Salt bridges: A:K.296

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.2, T.4, D.30, D.31, D.104 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.2, A:T.4, A:D.30, A:D.31, A:D.104 CA.4: 3 residues within 4Å: Chain A: T.128, Y.131, D.190 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.128, A:T.128, A:Y.131, A:D.190, H2O.6 CA.5: 5 residues within 4Å: Chain A: D.201, V.203, D.230, N.231, D.305 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.201, A:V.203, A:D.230, A:D.230, A:D.305 CA.6: 3 residues within 4Å: Chain A: T.324, Y.327, D.393 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.327, A:D.393, A:D.393, H2O.3, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stubbs, H.E. et al., Tandem sialoglycan-binding modules in a Streptococcus sanguinis serine-rich repeat adhesin create target dependent avidity effects. J.Biol.Chem. (2020)

Release Date

2020-08-26

Peptides

Adhesin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adhesin

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