SMTL ID : 6phx.1

SpAga D472N structure in complex with raffinose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x GLA- GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose-(1-6)-alpha-D-galactopyranose

GLA-GLC-FRU.1: 19 residues within 4Å: Chain A: Y.213, W.350, Y.354, D.380, D.381, W.425, R.457, K.490, N.492, N.494, C.539, G.541, G.542, W.558, D.561, H.594, Q.595 Chain B: A.72, F.73 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.561, A:Q.595, 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:R.457, A:D.561, A:H.594, A:D.561, A:R.457, B:D.70, B:D.70, B:D.70 GLA-GLC-FRU.9: 19 residues within 4Å: Chain A: A.72, F.73 Chain B: Y.213, W.350, Y.354, D.380, D.381, W.425, R.457, K.490, N.492, N.494, C.539, G.541, G.542, W.558, D.561, H.594, Q.595 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.561, B:Q.595, 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:R.457, B:D.561, B:H.594, B:D.561, B:R.457, A:D.70, A:D.70, A:D.70 GLA-GLC-FRU.17: 19 residues within 4Å: Chain C: Y.213, W.350, Y.354, D.380, D.381, W.425, R.457, K.490, N.492, N.494, C.539, G.541, G.542, W.558, D.561, H.594, Q.595 Chain D: A.72, F.73 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.561, C:Q.595, 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:N.494, C:D.561 Water bridges: C:Y.213, C:R.457, C:H.594, D:D.70, D:D.70, D:D.70, C:R.457 GLA-GLC-FRU.25: 19 residues within 4Å: Chain C: A.72, F.73 Chain D: Y.213, W.350, Y.354, D.380, D.381, W.425, R.457, K.490, N.492, N.494, C.539, G.541, G.542, W.558, D.561, H.594, Q.595 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.561, D:Q.595, 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:N.494, D:D.561 Water bridges: D:Y.213, D:R.457, D:H.594, D:R.457, C:D.70, C:D.70, C:D.70

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

TLA.2: 4 residues within 4Å: Chain A: H.139, L.335, S.336, R.552 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.336, A:R.552 Water bridges: A:H.139, A:S.140, A:E.337 Salt bridges: A:H.139, A:R.552 TLA.3: 4 residues within 4Å: Chain A: E.255, L.653, I.654, N.655 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:L.653, A:N.655, A:N.655 Water bridges: A:E.255, A:E.255, A:E.255, A:E.255, A:E.255, A:S.660, A:K.694 Salt bridges: A:K.694 TLA.10: 4 residues within 4Å: Chain B: H.139, L.335, S.336, R.552 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.336, B:R.552 Water bridges: B:H.139, B:S.140, B:E.337 Salt bridges: B:H.139, B:R.552 TLA.11: 4 residues within 4Å: Chain B: E.255, L.653, I.654, N.655 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:L.653, B:N.655, B:N.655 Water bridges: B:E.255, B:E.255, B:E.255, B:E.255, B:E.255, B:S.660, B:K.694 Salt bridges: B:K.694 TLA.18: 4 residues within 4Å: Chain C: H.139, L.335, S.336, R.552 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.336, C:R.552 Water bridges: C:H.139, C:S.140, C:E.337 Salt bridges: C:H.139, C:R.552 TLA.19: 4 residues within 4Å: Chain C: E.255, L.653, I.654, N.655 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:L.653, C:N.655, C:N.655 Water bridges: C:E.255, C:E.255, C:E.255, C:E.255, C:S.660, C:K.694 Salt bridges: C:K.694 TLA.26: 4 residues within 4Å: Chain D: H.139, L.335, S.336, R.552 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.336, D:R.552 Water bridges: D:H.139, D:S.140, D:E.337 Salt bridges: D:H.139, D:R.552 TLA.27: 4 residues within 4Å: Chain D: E.255, L.653, I.654, N.655 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:L.653, D:N.655, D:N.655 Water bridges: D:E.255, D:E.255, D:E.255, D:E.255, D:S.660, D:K.694 Salt bridges: D:K.694

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

EDO.4: 7 residues within 4Å: Chain A: L.50, H.52, L.53, D.198, F.199, P.200 Ligands: EDO.5 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: F.199, P.200, Y.204, F.261 Chain C: K.692 Ligands: EDO.4 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: V.591, L.602, R.605, L.618, L.623, E.627 Ligands: ACT.8 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain B: L.50, H.52, L.53, D.198, F.199, P.200 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: F.199, P.200, Y.204, F.261 Chain D: K.692 Ligands: EDO.12 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain B: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: V.591, L.602, R.605, L.618, L.623, E.627 Ligands: ACT.16 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain C: L.50, H.52, L.53, D.198, F.199, P.200 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: K.692 Chain C: F.199, P.200, Y.204, F.261 Ligands: EDO.20 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain C: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain C: V.591, L.602, R.605, L.618, L.623, E.627 Ligands: ACT.24 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain D: L.50, H.52, L.53, D.198, F.199, P.200 Ligands: EDO.29 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain B: K.692 Chain D: F.199, P.200, Y.204, F.261 Ligands: EDO.28 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain D: E.662, Y.677, R.679, V.683, E.688, T.689, V.723, L.725 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain D: V.591, L.602, R.605, L.618, L.623, E.627 Ligands: ACT.32 Ligand excluded by PLIP

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

ACT.8: 4 residues within 4Å: Chain A: P.601, L.602, R.605 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.602, A:R.605 Water bridges: A:E.603 ACT.16: 4 residues within 4Å: Chain B: P.601, L.602, R.605 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.602, B:R.605 Water bridges: B:E.603 ACT.24: 4 residues within 4Å: Chain C: P.601, L.602, R.605 Ligands: EDO.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.602, C:R.605 Water bridges: C:E.603 ACT.32: 4 residues within 4Å: Chain D: P.601, L.602, R.605 Ligands: EDO.31 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.602, D:R.605 Water bridges: D:E.603

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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