SMTL ID : 6phw.1

SpAga D472N structure in complex with melibiose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x GLC- GLA: alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose(Non-covalent)

GLC-GLA.1: 14 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 5 PLIP interactions: 5 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:N.492, A:G.542, A:W.558, A:Y.213, A:N.494 Water bridges: A:D.561, A:Q.595, A:Q.595 Salt bridges: A:R.457 GLC-GLA.13: 14 residues within 4Å: 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 5 PLIP interactions: 5 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:N.492, B:G.542, B:W.558, B:Y.213, B:N.494 Water bridges: B:D.561, B:Q.595, B:Q.595 Salt bridges: B:R.457 GLC-GLA.25: 14 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 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.381, C:R.457, C:R.457, C:K.490, C:K.490, C:N.492, C:G.542, C:W.558, C:Y.213, C:N.494 Water bridges: C:Q.595, C:Q.595 Salt bridges: C:R.457 GLC-GLA.37: 14 residues within 4Å: 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 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.381, D:R.457, D:R.457, D:K.490, D:K.490, D:N.492, D:G.542, D:W.558, D:Y.213, D:N.494 Water bridges: D:Q.595, D:Q.595 Salt bridges: D:R.457

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

TLA.2: 5 residues within 4Å: Chain A: H.139, L.335, S.336, R.552 Ligands: EDO.11 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.3: 5 residues within 4Å: Chain A: T.254, E.255, L.653, I.654, N.655 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.255, A:L.653, A:N.655, A:N.655 Water bridges: A:E.255, A:D.256, A:L.653, A:K.694 TLA.14: 5 residues within 4Å: Chain B: H.139, L.335, S.336, R.552 Ligands: EDO.23 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.15: 5 residues within 4Å: Chain B: T.254, E.255, L.653, I.654, N.655 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.255, B:L.653, B:N.655, B:N.655 Water bridges: B:E.255, B:D.256, B:L.653, B:K.694 TLA.26: 5 residues within 4Å: Chain C: H.139, L.335, S.336, R.552 Ligands: EDO.35 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.27: 5 residues within 4Å: Chain C: T.254, E.255, L.653, I.654, N.655 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.255, C:L.653, C:N.655, C:N.655 Water bridges: C:D.256, C:L.653, C:K.694 TLA.38: 5 residues within 4Å: Chain D: H.139, L.335, S.336, R.552 Ligands: EDO.47 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 TLA.39: 5 residues within 4Å: Chain D: T.254, E.255, L.653, I.654, N.655 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.255, D:L.653, D:N.655, D:N.655 Water bridges: D:D.256, D:L.653, D:K.694

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

EDO.4: 6 residues within 4Å: Chain A: L.50, H.52, L.53, D.198, F.199, P.200 Ligand excluded by PLIP EDO.5: 10 residues within 4Å: Chain A: N.130, G.131, S.137, P.138, M.141, T.165, A.174, S.175, Y.176, V.308 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: N.386, R.387, F.388, N.400, K.403 Ligand excluded by PLIP EDO.7: 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.8: 5 residues within 4Å: Chain A: A.202, D.203, K.277, N.281 Ligands: EDO.9 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: A.202, D.203, Y.204, Q.223, V.224, K.277, N.281, V.283 Ligands: EDO.8 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: R.24, I.25, I.125 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: S.140 Ligands: TLA.2 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: P.200, Y.204, F.261 Chain C: K.692 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: L.50, H.52, L.53, D.198, F.199, P.200 Ligand excluded by PLIP EDO.17: 10 residues within 4Å: Chain B: N.130, G.131, S.137, P.138, M.141, T.165, A.174, S.175, Y.176, V.308 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: N.386, R.387, F.388, N.400, K.403 Ligand excluded by PLIP EDO.19: 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.20: 5 residues within 4Å: Chain B: A.202, D.203, K.277, N.281 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain B: A.202, D.203, Y.204, Q.223, V.224, K.277, N.281, V.283 Ligands: EDO.20 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: R.24, I.25, I.125 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: S.140 Ligands: TLA.14 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: P.200, Y.204, F.261 Chain D: K.692 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain C: L.50, H.52, L.53, D.198, F.199, P.200 Ligand excluded by PLIP EDO.29: 10 residues within 4Å: Chain C: N.130, G.131, S.137, P.138, M.141, T.165, A.174, S.175, Y.176, V.308 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: N.386, R.387, F.388, N.400, K.403 Ligand excluded by PLIP EDO.31: 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.32: 5 residues within 4Å: Chain C: A.202, D.203, K.277, N.281 Ligands: EDO.33 Ligand excluded by PLIP EDO.33: 9 residues within 4Å: Chain C: A.202, D.203, Y.204, Q.223, V.224, K.277, N.281, V.283 Ligands: EDO.32 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain C: R.24, I.25, I.125 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain C: S.140 Ligands: TLA.26 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain A: K.692 Chain C: P.200, Y.204, F.261 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain D: L.50, H.52, L.53, D.198, F.199, P.200 Ligand excluded by PLIP EDO.41: 10 residues within 4Å: Chain D: N.130, G.131, S.137, P.138, M.141, T.165, A.174, S.175, Y.176, V.308 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain D: N.386, R.387, F.388, N.400, K.403 Ligand excluded by PLIP EDO.43: 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.44: 5 residues within 4Å: Chain D: A.202, D.203, K.277, N.281 Ligands: EDO.45 Ligand excluded by PLIP EDO.45: 9 residues within 4Å: Chain D: A.202, D.203, Y.204, Q.223, V.224, K.277, N.281, V.283 Ligands: EDO.44 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain D: R.24, I.25, I.125 Ligand excluded by PLIP EDO.47: 2 residues within 4Å: Chain D: S.140 Ligands: TLA.38 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain B: K.692 Chain D: P.200, Y.204, F.261 Ligand excluded by PLIP

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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