SMTL ID : 6gwg.1

Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose covalently linked to the nucleophile

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: G.18, S.19, H.20, M.21, E.179 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.18, A:H.20, A:M.21 Water bridges: A:G.18 Salt bridges: A:H.20 SO4.2: 4 residues within 4Å: Chain A: K.325, D.326, E.327, K.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.326, A:E.327 Salt bridges: A:K.325 SO4.3: 4 residues within 4Å: Chain A: F.414, W.415, G.416, E.417 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.415, A:G.416, A:E.417 SO4.4: 3 residues within 4Å: Chain A: E.457, K.458, T.459 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.458, A:T.459, A:T.459 SO4.5: 5 residues within 4Å: Chain A: R.109, Y.110, P.116, K.308, P.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.110 Salt bridges: A:R.109, A:K.308 SO4.6: 4 residues within 4Å: Chain A: N.182, R.509, Q.511 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.182, A:Q.511 Salt bridges: A:R.509 SO4.7: 2 residues within 4Å: Chain A: T.377, K.380 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.377 Water bridges: A:T.377, A:T.377, A:K.380 Salt bridges: A:K.380 SO4.8: 4 residues within 4Å: Chain A: N.182, L.185, R.509 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.182 Salt bridges: A:R.509

1 x FEK: (1~{S},2~{S},3~{S})-3-fluoranyl-6-(hydroxymethyl)cyclohex-5-ene-1,2,4-triol(Covalent)

FEK.9: 11 residues within 4Å: Chain A: W.88, W.213, Y.214, D.243, D.244, W.280, K.348, D.350, F.351, R.406, D.410 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.350, A:F.351 Hydrogen bonds: A:Y.214, A:D.244, A:K.348, A:K.348, A:R.406

3 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 1 residues within 4Å: Chain A: N.364 No protein-ligand interaction detected (PLIP) MG.11: 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.8, H2O.12 MG.12: 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.4, H2O.6, H2O.7, H2O.12

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: D.298, G.305, E.306 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.302, A:K.302, A:E.306 GOL.14: 3 residues within 4Å: Chain A: P.203, K.204, H.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.204, A:H.205 Water bridges: A:R.201

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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