SMTL ID : 6phv.1

SpAga galactose product complex structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 Ligands: EDO.7 Ligand excluded by PLIP EDO.2: 6 residues within 4Å: Chain A: L.50, H.52, L.53, D.198, F.199, P.200 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: V.591, R.605, L.618, E.627 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: Q.129, H.139, S.140, M.141 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: E.250, Q.251, G.252, V.253, A.257, G.258 Chain C: T.254, A.257 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: Q.316, H.323, Y.651 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: R.679, V.683, T.686, E.688, V.723, I.724, L.725 Chain C: R.69 Ligands: EDO.1 Ligand excluded by PLIP EDO.11: 9 residues within 4Å: Chain B: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 Ligands: EDO.17 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: L.50, H.52, L.53, D.198, F.199, P.200 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain B: V.591, R.605, L.618, E.627 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: Q.129, H.139, S.140, M.141 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain B: E.250, Q.251, G.252, V.253, A.257, G.258 Chain D: T.254, A.257 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: Q.316, H.323, Y.651 Ligand excluded by PLIP EDO.17: 9 residues within 4Å: Chain B: R.679, V.683, T.686, E.688, V.723, I.724, L.725 Chain D: R.69 Ligands: EDO.11 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain C: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 Ligands: EDO.27 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain C: L.50, H.52, L.53, D.198, F.199, P.200 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain C: V.591, R.605, L.618, E.627 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: Q.129, H.139, S.140, M.141 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain A: T.254, A.257 Chain C: E.250, Q.251, G.252, V.253, A.257, G.258 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: Q.316, H.323, Y.651 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain A: R.69 Chain C: R.679, V.683, T.686, E.688, V.723, I.724, L.725 Ligands: EDO.21 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain D: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 Ligands: EDO.37 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain D: L.50, H.52, L.53, D.198, F.199, P.200 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain D: V.591, R.605, L.618, E.627 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain D: Q.129, H.139, S.140, M.141 Ligand excluded by PLIP EDO.35: 8 residues within 4Å: Chain B: T.254, A.257 Chain D: E.250, Q.251, G.252, V.253, A.257, G.258 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain D: Q.316, H.323, Y.651 Ligand excluded by PLIP EDO.37: 9 residues within 4Å: Chain B: R.69 Chain D: R.679, V.683, T.686, E.688, V.723, I.724, L.725 Ligands: EDO.31 Ligand excluded by PLIP

4 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.8: 13 residues within 4Å: Chain A: W.350, D.380, D.381, W.425, R.457, K.490, D.492, N.494, C.539, G.541, G.542, W.558, D.561 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.381, A:D.381, A:R.457, A:R.457, A:K.490, A:K.490, A:D.492, A:N.494, A:G.542, A:W.558, A:D.561 Water bridges: A:D.561 Salt bridges: A:R.457 GLA.18: 13 residues within 4Å: Chain B: W.350, D.380, D.381, W.425, R.457, K.490, D.492, N.494, C.539, G.541, G.542, W.558, D.561 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:D.381, B:D.381, B:R.457, B:R.457, B:K.490, B:K.490, B:D.492, B:N.494, B:G.542, B:W.558, B:D.561 Water bridges: B:D.561 Salt bridges: B:R.457 GLA.28: 13 residues within 4Å: Chain C: W.350, D.380, D.381, W.425, R.457, K.490, D.492, N.494, C.539, G.541, G.542, W.558, D.561 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:D.381, C:R.457, C:R.457, C:K.490, C:K.490, C:D.492, C:N.494, C:G.542, C:W.558, C:D.561 Salt bridges: C:R.457 GLA.38: 13 residues within 4Å: Chain D: W.350, D.380, D.381, W.425, R.457, K.490, D.492, N.494, C.539, G.541, G.542, W.558, D.561 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:D.381, D:R.457, D:R.457, D:K.490, D:K.490, D:D.492, D:N.494, D:G.542, D:W.558, D:D.561 Salt bridges: D:R.457

4 x NA: SODIUM ION(Non-functional Binders)

NA.9: 3 residues within 4Å: Chain A: P.132, L.135, S.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.135 Water bridges: A:G.134, A:S.137 NA.19: 3 residues within 4Å: Chain B: P.132, L.135, S.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.132 Water bridges: B:G.134, B:S.137 NA.29: 3 residues within 4Å: Chain C: P.132, L.135, S.137 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:P.132 Water bridges: C:G.134, C:S.137 NA.39: 3 residues within 4Å: Chain D: P.132, L.135, S.137 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.132 Water bridges: D:G.134, D:S.137

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

TRS.10: 6 residues within 4Å: Chain A: V.399, E.401, S.407, L.408, E.409, H.484 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.401, A:E.401, A:L.408, A:E.409, A:H.484 TRS.20: 6 residues within 4Å: Chain B: V.399, E.401, S.407, L.408, E.409, H.484 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.401, B:E.401, B:L.408, B:E.409, B:H.484 TRS.30: 6 residues within 4Å: Chain C: V.399, E.401, S.407, L.408, E.409, H.484 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.401, C:L.408, C:E.409, C:H.484 TRS.40: 6 residues within 4Å: Chain D: V.399, E.401, S.407, L.408, E.409, H.484 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.401, D:L.408, D:E.409, D:H.484

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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