SMTL ID : 6gta.1

Alpha-galactosidase mutant D378A from Thermotoga maritima in complex with intact cyclohexene-based carbasugar mimic of galactose with 3,5 difluorophenyl leaving group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

3 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.415, A:G.416, A:E.417, A:H.418 SO4.2: 4 residues within 4Å: Chain A: K.325, D.326, E.327, K.362 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.326, A:E.327, A:E.327 Salt bridges: A:K.325, A:K.362 SO4.3: 3 residues within 4Å: Chain A: E.457, K.458, T.459 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.458, A:T.459

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 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.3, H2O.4, H2O.5, H2O.6 MG.5: 1 residues within 4Å: Chain A: E.25 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.25, H2O.1, H2O.1

1 x F9W: (1~{R},2~{S},3~{S},6~{S})-6-[3,5-bis(fluoranyl)phenoxy]-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol(Non-covalent)

F9W.6: 14 residues within 4Å: Chain A: W.88, W.108, W.213, Y.214, D.243, D.244, W.280, W.314, K.348, D.350, F.351, C.391, R.406, P.425 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.351 Hydrogen bonds: A:W.88, A:Y.214, A:Y.214, A:D.244, A:D.244, A:K.348, A:K.348, A:D.350, A:R.406, A:R.406 pi-Stacking: A:W.88

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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