SMTL ID : 2yfn.1

galactosidase domain of alpha-galactosidase-sucrose kinase, AgaSK

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: R.220, L.279, A.484, D.485, V.486 Chain D: L.80, G.81, T.82, G.83, D.84, Y.85 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:R.220, A:R.220, A:D.485, A:V.486, D:G.81, D:G.83 Water bridges: A:V.486, D:G.81, D:D.84 GOL.2: 8 residues within 4Å: Chain A: Y.36, F.185, Q.187, F.190, E.236, Y.247 Chain C: R.672, H.698 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.187, A:Q.187, A:Y.247 Water bridges: A:Y.36, A:S.245, C:R.672 GOL.7: 11 residues within 4Å: Chain B: R.220, L.279, A.484, D.485, V.486 Chain C: L.80, G.81, T.82, G.83, D.84, Y.85 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.220, B:R.220, B:D.485, B:V.486, C:G.81, C:G.83 Water bridges: B:V.486, C:G.81, C:D.84 GOL.8: 8 residues within 4Å: Chain B: Y.36, F.185, Q.187, F.190, E.236, Y.247 Chain D: R.672, H.698 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.187, B:Q.187, B:Y.247, B:Y.247 Water bridges: B:Y.36, B:S.245, D:R.672 GOL.13: 11 residues within 4Å: Chain B: L.80, G.81, T.82, G.83, D.84, Y.85 Chain C: R.220, L.279, A.484, D.485, V.486 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:G.81, B:G.83, C:R.220, C:R.220, C:D.485, C:V.486 Water bridges: B:G.81, B:D.84, C:V.486 GOL.14: 8 residues within 4Å: Chain A: R.672, H.698 Chain C: Y.36, F.185, Q.187, F.190, E.236, Y.247 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Water bridges: A:R.672, C:Y.36, C:S.245 Hydrogen bonds: C:Q.187, C:Q.187, C:Y.247, C:Y.247 GOL.19: 11 residues within 4Å: Chain A: L.80, G.81, T.82, G.83, D.84, Y.85 Chain D: R.220, L.279, A.484, D.485, V.486 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:G.81, A:G.83, D:R.220, D:R.220, D:D.485, D:V.486 Water bridges: A:G.81, A:D.84, D:V.486 GOL.20: 8 residues within 4Å: Chain B: R.672, H.698 Chain D: Y.36, F.185, Q.187, F.190, E.236, Y.247 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.187, D:Q.187, D:Y.247 Water bridges: D:Y.36, D:S.245, B:R.672

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

EDO.3: 3 residues within 4Å: Chain A: P.27, A.62, D.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.65 EDO.9: 3 residues within 4Å: Chain B: P.27, A.62, D.65 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.65, B:D.65 EDO.15: 3 residues within 4Å: Chain C: P.27, A.62, D.65 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.65, C:D.65 EDO.21: 3 residues within 4Å: Chain D: P.27, A.62, D.65 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.65

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: R.111, Y.115, R.116, R.164 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.116, A:R.116 Water bridges: A:R.111, A:R.111 Salt bridges: A:R.111, A:R.164 PO4.10: 4 residues within 4Å: Chain B: R.111, Y.115, R.116, R.164 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.116, B:R.116 Water bridges: B:R.111, B:R.111 Salt bridges: B:R.111, B:R.164 PO4.16: 4 residues within 4Å: Chain C: R.111, Y.115, R.116, R.164 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.116, C:R.116 Water bridges: C:R.111, C:R.111 Salt bridges: C:R.111, C:R.164 PO4.22: 4 residues within 4Å: Chain D: R.111, Y.115, R.116, R.164 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.116, D:R.116 Water bridges: D:R.111, D:R.111 Salt bridges: D:R.111, D:R.164

8 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: E.176, E.277, F.280, S.281 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.176, A:E.176, A:E.277, A:F.280, H2O.20 MG.6: 1 residues within 4Å: Chain A: E.277 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.277, H2O.7, H2O.20, H2O.20, H2O.21, H2O.21 MG.11: 4 residues within 4Å: Chain B: E.176, E.277, F.280, S.281 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.176, B:E.176, B:E.277, B:F.280, H2O.61 MG.12: 1 residues within 4Å: Chain B: E.277 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.277, H2O.48, H2O.61, H2O.61, H2O.61, H2O.61 MG.17: 4 residues within 4Å: Chain C: E.176, E.277, F.280, S.281 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.176, C:E.176, C:E.277, C:F.280, H2O.102 MG.18: 1 residues within 4Å: Chain C: E.277 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.277, H2O.89, H2O.102, H2O.102, H2O.102, H2O.102 MG.23: 4 residues within 4Å: Chain D: E.176, E.277, F.280, S.281 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.176, D:E.176, D:E.277, D:F.280, H2O.142 MG.24: 1 residues within 4Å: Chain D: E.277 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.277, H2O.129, H2O.142, H2O.143, H2O.143, H2O.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruel, L. et al., Agask, a Bifunctional Enzyme from the Human Microbiome Coupling Galactosidase and Kinase Activities. J.Biol.Chem. (2011)

Release Date

2011-09-28

Peptides

ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK

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