SMTL ID : 6vs7.1 (1 other biounit)

Sialic acid binding region of Streptococcus Sanguinis SK1 adhesin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.2, T.4, D.30, D.104 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.10 CA.2: 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:T.324, A:Y.327, A:D.393, H2O.12, H2O.15 CA.3: 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:D.201, A:V.203, A:D.230, A:D.230 CA.4: 3 residues within 4Å: Chain A: T.128, Y.131, 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.7, H2O.14

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

SO4.5: 3 residues within 4Å: Chain A: Q.402, D.403, R.407 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.402, A:Q.402, A:R.407 Water bridges: A:D.403 SO4.6: 3 residues within 4Å: Chain A: R.212, E.225, H.227 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.212, A:R.212, A:R.212, A:E.225, A:H.227 Salt bridges: A:R.212, A:H.227 SO4.7: 2 residues within 4Å: Chain A: R.357, T.361 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.357 SO4.8: 2 residues within 4Å: Chain A: R.18, V.90 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.18, A:R.18, A:R.18, A:V.90, A:V.90 Salt bridges: A:R.18

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.10: 2 residues within 4Å: Chain A: G.362, N.366 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.366 Water bridges: A:G.362, A:G.362, A:N.366, A:N.366

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

EDO.11: 2 residues within 4Å: Chain A: A.46, D.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.47 EDO.12: 1 residues within 4Å: Chain A: R.392 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.392, A:R.392 EDO.13: 2 residues within 4Å: Chain A: N.330, N.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.330, A:N.363 Water bridges: A:N.363 EDO.14: 3 residues within 4Å: Chain A: N.261, T.280, R.282 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.261 Water bridges: A:T.259, A:N.261, A:T.280, A:R.282 EDO.15: 3 residues within 4Å: Chain A: T.272, Q.274, N.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.275 Water bridges: A:T.272, A:Q.274

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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