SMTL ID : 2wvt.1

Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron in complex with a novel iminosugar fucosidase inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FHN: (2S,3R,5R,6S)-3,4,5-TRIHYDROXY-2,6-BIS(HYDROXYMETHYL)PIPERIDINIUM(Non-covalent)

FHN.1: 13 residues within 4Å: Chain A: H.36, E.57, W.58, H.105, H.106, Y.148, W.197, D.199, W.202, R.232, E.258, C.278, W.286 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.58, A:W.58, A:H.105, A:Y.148, A:D.199, A:R.232, A:E.258 FHN.6: 14 residues within 4Å: Chain B: H.36, E.57, W.58, H.105, H.106, Y.148, W.197, D.199, W.202, R.232, E.258, C.278, W.286 Ligands: GOL.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.57, B:W.58, B:W.58, B:H.105, B:R.232, B:E.258

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: W.202, R.232, R.241, H.242, G.256 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.232, A:R.241 Water bridges: A:D.199 GOL.3: 4 residues within 4Å: Chain A: E.254, G.256, Y.257, R.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.256, A:G.256, A:R.260 GOL.7: 8 residues within 4Å: Chain B: A.55, E.57, W.58, W.62, N.284, W.286 Ligands: FHN.6, IMD.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.57, B:N.284 Water bridges: B:R.259 GOL.8: 5 residues within 4Å: Chain A: D.363 Chain B: V.265, K.361, Q.362, D.363 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.361, B:D.363 Water bridges: B:K.361, A:D.363 GOL.9: 6 residues within 4Å: Chain A: D.363 Chain B: D.305, K.361, G.365, Y.366, N.381 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.361, B:G.365, B:Y.366, B:N.381 Water bridges: A:D.363, A:D.363

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 2 residues within 4Å: Chain A: W.58, W.202 2 PLIP interactions: 2 interactions with chain A pi-Stacking: A:W.202, A:W.202 IMD.5: 2 residues within 4Å: Chain A: K.342, R.346 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.346 IMD.10: 2 residues within 4Å: Chain B: W.202 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain B pi-Stacking: B:W.202, B:W.202 IMD.11: 4 residues within 4Å: Chain B: K.60, S.61, W.154, Y.161 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.61, B:Y.161 pi-Stacking: B:W.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lammerts Van Bueren, A. et al., Analysis of the Reaction Coordinate of Alpha-L-Fucosidases: A Combined Structural and Quantum Mechanical Approach. J.Am.Chem.Soc. (2010)

Release Date

2010-02-02

Peptides

ALPHA-L-FUCOSIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ALPHA-L-FUCOSIDASE

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