SMTL ID : 6vt2.1 (1 other biounit)

Sialic acid binding region of Streptococcus sanguinis SK1 adhesin bound to sTa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

2 x A2G- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose

A2G-GAL-SIA.1: 13 residues within 4Å: Chain A: L.244, A.245, S.248, T.249, T.252, L.289, G.294, G.295, K.296, Y.297, T.298, K.300, F.320 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:L.244, A:S.248, A:K.296, A:T.298, A:T.298 Water bridges: A:L.244, A:S.248, A:T.249, A:T.298, A:T.298, A:K.300, A:S.248, A:S.248, A:K.296, A:K.296, A:T.298 Hydrophobic interactions: A:Y.297, A:F.320 Salt bridges: A:K.296 A2G-GAL-SIA.2: 14 residues within 4Å: Chain A: I.43, E.44, D.53, P.54, H.88, G.93, D.94, R.95, Y.96, T.97, K.98, Y.99, D.114, K.115 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.44, A:Y.99, A:Y.99, A:D.53, A:R.95, A:T.97, A:T.97, A:K.98 Hydrophobic interactions: A:Y.96

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: T.324, Y.327, T.328, P.329, D.393 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.324, A:Y.327, A:D.393, H2O.17, H2O.20 CA.4: 6 residues within 4Å: Chain A: D.2, T.4, D.30, S.32, D.104, N.108 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.2, A:T.4, A:D.30, A:D.104, H2O.18 CA.5: 6 residues within 4Å: Chain A: T.128, Y.131, T.132, P.133, Y.184, D.190 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.128, A:Y.131, A:D.190, H2O.17, H2O.20 CA.6: 8 residues within 4Å: Chain A: D.201, V.203, A.204, D.230, N.231, S.232, D.305, L.309 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.201, A:D.201, A:V.203, A:D.230, A:D.230

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: Q.402, D.403, R.407 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.402, A:Q.402, A:R.407 Water bridges: A:D.403, A:D.403 SO4.8: 3 residues within 4Å: Chain A: R.37, I.39, T.50 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.37, A:R.37, A:R.37, A:R.37, A:T.50 Salt bridges: A:R.37

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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