SMTL ID : 6gvd.1

Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

monomer

Ligands

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

SO4.1: 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 SO4.2: 4 residues within 4Å: Chain A: F.414, W.415, G.416, E.417 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.415, A:G.416, A:E.417 Water bridges: A:R.541

3 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.2, H2O.10, H2O.14, H2O.16 MG.4: 1 residues within 4Å: Chain A: E.265 No protein-ligand interaction detected (PLIP) MG.5: 6 residues within 4Å: Chain A: R.406, I.407, G.408, D.448, P.449, D.450 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.448, H2O.8

1 x FDK: (1~{S},2~{S},3~{S},4~{S})-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol(Non-covalent)

FDK.6: 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: 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

Ren, W. et al., Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level. Nat Commun (2018)

Release Date

2018-08-22

Peptides

Alpha-galactosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-galactosidase

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