SMTL ID : 6phu.1

SpAga wild type apo structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: L.50, H.52, L.53, D.198, F.199, P.200 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.52, A:L.53, A:D.198 Water bridges: A:L.53, A:L.53, A:N.64 EDO.2: 8 residues within 4Å: Chain A: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.679, A:R.679, A:T.689, A:T.689 EDO.4: 6 residues within 4Å: Chain B: L.50, H.52, L.53, D.198, F.199, P.200 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.52, B:L.53, B:D.198 Water bridges: B:L.53, B:L.53, B:N.64 EDO.5: 8 residues within 4Å: Chain B: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.679, B:R.679, B:T.689, B:T.689 EDO.7: 6 residues within 4Å: Chain C: L.50, H.52, L.53, D.198, F.199, P.200 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.52, C:L.53, C:D.198 Water bridges: C:N.64, C:N.64 EDO.8: 8 residues within 4Å: Chain C: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.679, C:R.679, C:T.689, C:T.689, C:T.689 Water bridges: C:E.688 EDO.10: 6 residues within 4Å: Chain D: L.50, H.52, L.53, D.198, F.199, P.200 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.52, D:L.53, D:D.198 Water bridges: D:N.64, D:N.64 EDO.11: 8 residues within 4Å: Chain D: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.679, D:R.679, D:T.689, D:T.689, D:T.689 Water bridges: D:E.688

4 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.3: 4 residues within 4Å: Chain A: H.139, L.335, S.336, R.552 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.336 Water bridges: A:E.337 Salt bridges: A:H.139, A:R.552 TLA.6: 4 residues within 4Å: Chain B: H.139, L.335, S.336, R.552 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.336 Water bridges: B:E.337 Salt bridges: B:H.139, B:R.552 TLA.9: 4 residues within 4Å: Chain C: H.139, L.335, S.336, R.552 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.336 Water bridges: C:E.337 Salt bridges: C:H.139, C:R.552 TLA.12: 4 residues within 4Å: Chain D: H.139, L.335, S.336, R.552 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.336 Water bridges: D:E.337 Salt bridges: D:H.139, D:R.552

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hobbs, J.K. et al., Molecular analysis of an enigmaticStreptococcus pneumoniaevirulence factor: The raffinose-family oligosaccharide utilization system. J.Biol.Chem. (2019)

Release Date

2019-10-02

Peptides

Alpha-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Alpha-galactosidase

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