SMTL ID : 4fns.1

Crystal structure of GH36 alpha-galactosidase AgaA A355E from Geobacillus stearothermophilus in complex with 1-deoxygalactonojirimycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x DGJ: (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)

DGJ.1: 13 residues within 4Å: Chain A: W.336, D.366, D.367, W.411, R.443, K.476, D.478, N.480, C.526, G.528, G.529, W.545, D.548 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.367, A:D.367, A:R.443, A:R.443, A:K.476, A:K.476, A:N.480, A:N.480, A:G.529, A:W.545 Water bridges: A:D.548 DGJ.4: 13 residues within 4Å: Chain B: W.336, D.366, D.367, W.411, R.443, K.476, D.478, N.480, C.526, G.528, G.529, W.545, D.548 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.367, B:R.443, B:R.443, B:K.476, B:K.476, B:D.478, B:N.480, B:N.480, B:G.529, B:W.545 Water bridges: B:D.548 DGJ.7: 13 residues within 4Å: Chain C: W.336, D.366, D.367, W.411, R.443, K.476, D.478, N.480, C.526, G.528, G.529, W.545, D.548 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:D.367, C:D.367, C:R.443, C:R.443, C:K.476, C:K.476, C:N.480, C:N.480, C:G.529, C:W.545 DGJ.10: 13 residues within 4Å: Chain D: W.336, D.366, D.367, W.411, R.443, K.476, D.478, N.480, C.526, G.528, G.529, W.545, D.548 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:D.367, D:R.443, D:R.443, D:K.476, D:K.476, D:N.480, D:N.480, D:G.528, D:G.529, D:W.545

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

SO4.2: 9 residues within 4Å: Chain A: G.200, R.201, W.204, N.549, S.554, V.583 Chain C: A.670, E.671, A.672 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:E.671, C:A.672, C:A.672, A:N.549, A:S.554, A:S.554 SO4.3: 7 residues within 4Å: Chain A: K.105, G.138, D.139, A.140, G.143, L.144, E.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.139, A:E.145, A:E.145 Water bridges: A:G.143 SO4.5: 9 residues within 4Å: Chain B: G.200, R.201, W.204, N.549, S.554, V.583 Chain D: A.670, E.671, A.672 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:A.670, D:A.672, B:N.549 Water bridges: B:R.585 SO4.6: 7 residues within 4Å: Chain B: K.105, G.138, D.139, A.140, G.143, L.144, E.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.139, B:D.139 SO4.8: 8 residues within 4Å: Chain A: A.670, E.671, A.672 Chain C: G.200, R.201, W.204, N.549, S.554 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.672, A:A.672, C:N.549, C:S.554 SO4.9: 7 residues within 4Å: Chain C: K.105, G.138, D.139, A.140, G.143, L.144, E.145 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.139, C:G.143 Salt bridges: C:K.105 SO4.12: 9 residues within 4Å: Chain B: A.670, E.671, A.672 Chain D: G.200, R.201, W.204, N.549, S.554, V.583 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.549, B:A.672 SO4.13: 7 residues within 4Å: Chain D: K.105, G.138, D.139, G.143, L.144, E.145, K.168 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.139, D:D.139 Salt bridges: D:K.105

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

EDO.11: 4 residues within 4Å: Chain D: L.176, P.277, F.280, T.281 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.280 Water bridges: D:R.177, D:R.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Merceron, R. et al., The molecular mechanism of the thermostable alpha-galactosidases AgaA and AgaB explained by X-ray crystallography and mutational studies. J.Biol.Chem. (2012)

Release Date

2012-10-03

Peptides

Alpha-galactosidase AgaA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Alpha-galactosidase AgaA

Related Entries With Identical Sequence