SMTL ID : 5m1i.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: G.18, S.19, H.20, M.21, K.134 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.18, A:S.19, A:H.20, A:M.21 Water bridges: A:G.18, A:G.18 Salt bridges: A:H.20, A:K.134 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 SO4.3: 4 residues within 4Å: Chain A: F.414, W.415, G.416, E.417 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.415, A:G.416, A:E.417 Water bridges: A:E.417, A:E.417, A:H.418 SO4.4: 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 SO4.5: 3 residues within 4Å: Chain A: K.142, R.372, E.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.376 Salt bridges: A:R.372 SO4.6: 4 residues within 4Å: Chain A: E.165, F.166, D.167, D.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.167, A:D.168, A:D.168

1 x 7D8: (1~{R},2~{S},3~{S},4~{S},6~{R})-4-fluoranyl-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3-diol(Covalent)

7D8.7: 12 residues within 4Å: Chain A: W.88, W.213, Y.214, D.243, D.244, W.280, K.348, D.350, F.351, C.391, R.406, D.410 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.88, A:D.350, A:F.351 Hydrogen bonds: A:Y.214, A:D.244, A:K.348, A:K.348, A:R.406

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 7 residues within 4Å: Chain A: W.88, P.409, D.410, G.423, A.424, P.425 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.410 EDO.9: 6 residues within 4Å: Chain A: W.88, W.108, T.111, G.423 Ligands: EDO.8, EDO.12 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain A: V.15, P.16, A.22, T.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.16 EDO.11: 3 residues within 4Å: Chain A: P.203, K.204, H.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.204, A:H.205 EDO.12: 9 residues within 4Å: Chain A: Q.86, W.88, G.89, T.111, A.112, N.422, G.423 Ligands: EDO.9, EDO.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.86, A:W.88, A:T.111 EDO.13: 1 residues within 4Å: Chain A: K.380 No protein-ligand interaction detected (PLIP) EDO.14: 2 residues within 4Å: Chain A: H.10, S.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.10, A:S.11 EDO.15: 4 residues within 4Å: Chain A: K.51, I.52, H.53, L.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.53, A:L.54 EDO.16: 7 residues within 4Å: Chain A: E.103, I.104, D.105, W.108, T.111, A.112 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.103, A:D.105 EDO.17: 5 residues within 4Å: Chain A: P.207, I.276, R.345, D.385, F.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.385 EDO.18: 2 residues within 4Å: Chain A: R.257, G.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.258 EDO.19: 6 residues within 4Å: Chain A: R.68, V.118, N.122, A.149, E.151, Y.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.68, A:N.122, A:E.151

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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