SMTL ID : 5m16.1

Structure of GH36 alpha-galactosidase from Thermotoga maritima in complex with a hydrolysed cyclopropyl carbasugar.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: F.414, W.415, G.416, E.417, H.418 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.415, A:G.416, A:E.417 Water bridges: A:H.418, A:I.419 SO4.2: 4 residues within 4Å: Chain A: K.325, D.326, E.327, K.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.326, A:E.327 Salt bridges: A:K.325, A:K.362

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: H.441, D.442, D.477 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.442, A:D.477, H2O.1, H2O.9, H2O.10, H2O.10

1 x 7D2: (1~{R},2~{S},3~{S},4~{S},5~{S},6~{S})-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3,4,5-tetrol(Non-covalent)

7D2.4: 13 residues within 4Å: Chain A: W.88, W.213, Y.214, D.243, D.244, W.280, W.314, K.348, D.350, F.351, C.391, R.406, D.410 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.213, A:F.351 Hydrogen bonds: A:Y.214, A:D.244, A:D.244, A:K.348, A:K.348, A:D.350, A:R.406, A:R.406, A:D.410

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adamson, C. et al., Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars. Angew.Chem.Int.Ed.Engl. (2016)

Release Date

2016-11-09

Peptides

Alpha-galactosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-galactosidase

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