SMTL ID : 6pi0.1

AgaD472N-Linear Blood group B type 2 trisaccharide complex structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

4 x GAL- GLA: alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose(Non-covalent)

GAL-GLA.1: 15 residues within 4Å: Chain A: Y.213, W.350, D.380, D.381, W.425, R.457, K.490, N.492, N.494, C.539, G.541, G.542, W.558, D.561 Chain B: F.73 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Water bridges: B:D.70, B:D.70, A:W.350, A:R.457, A:D.561 Hydrogen bonds: A:Y.213, A:N.494, A:N.494, A:D.381, A:D.381, A:R.457, A:R.457, A:K.490, A:K.490, A:N.492, A:G.542, A:W.558 Salt bridges: A:R.457 GAL-GLA.11: 15 residues within 4Å: Chain A: F.73 Chain B: Y.213, W.350, D.380, D.381, W.425, R.457, K.490, N.492, N.494, C.539, G.541, G.542, W.558, D.561 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.213, B:N.494, B:N.494, B:D.381, B:D.381, B:R.457, B:R.457, B:K.490, B:K.490, B:N.492, B:G.542, B:W.558 Water bridges: B:W.350, B:R.457, A:D.70, A:D.70, B:D.561 Salt bridges: B:R.457 GAL-GLA.21: 15 residues within 4Å: Chain C: Y.213, W.350, D.380, D.381, W.425, R.457, K.490, N.492, N.494, C.539, G.541, G.542, W.558, D.561 Chain D: F.73 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.494, C:N.494, C:D.381, C:R.457, C:R.457, C:K.490, C:K.490, C:N.492, C:G.542, C:W.558 Water bridges: C:W.350, C:R.457, D:D.70, D:D.70 Salt bridges: C:R.457 GAL-GLA.31: 15 residues within 4Å: Chain C: F.73 Chain D: Y.213, W.350, D.380, D.381, W.425, R.457, K.490, N.492, N.494, C.539, G.541, G.542, W.558, D.561 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.494, D:N.494, D:D.381, D:R.457, D:R.457, D:K.490, D:K.490, D:N.492, D:G.542, D:W.558 Water bridges: D:W.350, D:R.457, C:D.70, C:D.70 Salt bridges: D:R.457

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

TLA.2: 4 residues within 4Å: Chain A: H.139, L.335, S.336, R.552 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.336, A:R.552 Water bridges: A:E.337 Salt bridges: A:H.139, A:R.552 TLA.12: 4 residues within 4Å: Chain B: H.139, L.335, S.336, R.552 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.336, B:R.552 Water bridges: B:E.337 Salt bridges: B:H.139, B:R.552 TLA.22: 4 residues within 4Å: Chain C: H.139, L.335, S.336, R.552 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.336, C:R.552 Water bridges: C:E.337 Salt bridges: C:H.139, C:R.552 TLA.32: 4 residues within 4Å: Chain D: H.139, L.335, S.336, R.552 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.336, D:R.552 Water bridges: D:E.337 Salt bridges: D:H.139, D:R.552

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

EDO.3: 7 residues within 4Å: Chain A: L.50, H.52, L.53, D.198, F.199, P.200 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: P.200, Y.204, F.261 Chain C: K.692 Ligands: EDO.3 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: E.662, Y.677, R.679, E.688, T.689, V.723, L.725 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: V.591, L.602, R.605, L.618, L.623, E.627 Ligands: ACT.10 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: L.29, E.42, K.51, K.61, G.62, S.65 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: T.254, A.257 Chain C: E.250, Q.251, G.252, V.253, A.257 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: N.661, S.682 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain B: L.50, H.52, L.53, D.198, F.199, P.200 Ligands: EDO.14 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: P.200, Y.204, F.261 Chain D: K.692 Ligands: EDO.13 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: E.662, Y.677, R.679, E.688, T.689, V.723, L.725 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: V.591, L.602, R.605, L.618, L.623, E.627 Ligands: ACT.20 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: L.29, E.42, K.51, K.61, G.62, S.65 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: T.254, A.257 Chain D: E.250, Q.251, G.252, V.253, A.257 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: N.661, S.682 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain C: L.50, H.52, L.53, D.198, F.199, P.200 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: K.692 Chain C: P.200, Y.204, F.261 Ligands: EDO.23 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain C: E.662, Y.677, R.679, E.688, T.689, V.723, L.725 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain C: V.591, L.602, R.605, L.618, L.623, E.627 Ligands: ACT.30 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain C: L.29, E.42, K.51, K.61, G.62, S.65 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain A: E.250, Q.251, G.252, V.253, A.257 Chain C: T.254, A.257 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain C: N.661, S.682 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain D: L.50, H.52, L.53, D.198, F.199, P.200 Ligands: EDO.34 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain B: K.692 Chain D: P.200, Y.204, F.261 Ligands: EDO.33 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain D: E.662, Y.677, R.679, E.688, T.689, V.723, L.725 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain D: V.591, L.602, R.605, L.618, L.623, E.627 Ligands: ACT.40 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain D: L.29, E.42, K.51, K.61, G.62, S.65 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain B: E.250, Q.251, G.252, V.253, A.257 Chain D: T.254, A.257 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain D: N.661, S.682 Ligand excluded by PLIP

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 4 residues within 4Å: Chain A: P.601, L.602, R.605 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.602 Hydrogen bonds: A:L.602 Water bridges: A:R.605 ACT.20: 4 residues within 4Å: Chain B: P.601, L.602, R.605 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.602 Hydrogen bonds: B:L.602 Water bridges: B:R.605 ACT.30: 4 residues within 4Å: Chain C: P.601, L.602, R.605 Ligands: EDO.26 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.602 Hydrogen bonds: C:L.602 Water bridges: C:R.605 ACT.40: 4 residues within 4Å: Chain D: P.601, L.602, R.605 Ligands: EDO.36 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.602 Hydrogen bonds: D:L.602 Water bridges: D:R.605

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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