SMTL ID : 6gwf.1

Alpha-galactosidase mutant D387A from Thermotoga maritima in complex with intact cyclohexene-based carbasugar mimic of galactose with 2,4-dinitro leaving group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.32, F.36 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.32 Salt bridges: A:R.32 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 FEQ: (1~{S},2~{S},5~{S},6~{R})-5-(2,4-dinitrophenoxy)-6-fluoranyl-3-(hydroxymethyl)cyclohex-3-ene-1,2-diol(Non-covalent)

FEQ.3: 15 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, A.410, P.425 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.351, A:P.425 Hydrogen bonds: A:W.213, A:Y.214, A:D.244, A:K.348, A:K.348, A:R.406 pi-Stacking: A:W.88 Halogen bonds: A:R.406

1 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.2, H2O.9, H2O.10, H2O.11

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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