SMTL ID : 5h41.1 (1 other biounit)

Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with sophorose, isofagomine, sulfate ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x GLC- BGC: beta-D-glucopyranose-(1-2)-alpha-D-glucopyranose(Non-covalent)

GLC-BGC.1: 12 residues within 4Å: Chain A: Y.142, Q.622, G.625, D.632, W.671, D.761, R.908, R.917, E.918, W.1002, Y.1005 Ligands: IFM.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.622, A:R.908, A:R.908, A:R.917, A:E.918, A:E.918, A:Q.622, A:G.625 Water bridges: A:E.918, A:E.918, A:Q.622, A:D.761, A:Y.1005

1 x IFM: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE(Non-covalent)

IFM.2: 10 residues within 4Å: Chain A: R.631, D.632, W.759, D.760, D.761, E.918, Y.923 Ligands: GLC-BGC.1, GLC-BGC.1, SO4.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.923 Hydrogen bonds: A:R.631, A:R.631, A:D.760, A:D.761, A:E.918, A:Y.923 Water bridges: A:D.632, A:D.632, A:Q.670, A:Q.670, A:R.917

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: Y.923, H.925, S.1006, S.1007 Ligands: IFM.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.1007 Water bridges: A:H.613, A:D.632, A:R.917, A:R.917, A:R.917, A:Y.970 Salt bridges: A:H.925 SO4.4: 3 residues within 4Å: Chain A: R.1024, H.1031, L.1082 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.1024, A:H.1031

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakajima, M. et al., Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans. Sci Rep (2017)

Release Date

2017-03-01

Peptides

Uncharacterized protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uncharacterized protein

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