SMTL ID : 6hzy.1

Crystal structure of a bacterial fucosidase with inhibitor FucPUG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: D.326, K.382, D.384, G.386, Y.387, F.401, N.402 Chain B: D.384 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: N.393, D.394, E.395, K.459, V.460 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: A.54, W.108, M.111, A.112, Y.159, F.350 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: E.420, I.431, T.432, V.433 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: G.70, K.71, V.72 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: K.382, Q.383, D.384 Chain B: D.384 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: T.34, N.35, R.39, K.242, D.273 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: W.68, N.69, A.84, K.85, V.86, P.87, E.90 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: K.311, D.312, W.313, S.314, R.351, E.353 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: K.228, R.262 Ligands: SO4.16 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: A.360, K.363, W.364, E.452 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: A.105, K.106, E.154, K.157, A.158 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: K.106, A.109, K.110, A.158, D.161, E.162 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: A.54, W.108, M.111, A.112, Y.159, F.342, F.350 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: Y.180, R.181, Y.182, D.183 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: K.355, A.356, T.359 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: T.34, N.35, R.39, E.238, K.242, D.273 Ligand excluded by PLIP

2 x GYZ: [(~{Z})-[(3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-ylidene]amino] ~{N}-phenylcarbamate(Non-covalent)

GYZ.12: 13 residues within 4Å: Chain A: H.57, E.78, W.79, H.126, H.127, Y.169, W.218, D.220, R.253, G.277, E.279, W.307 Ligands: SO4.16 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.218, A:E.279 Hydrogen bonds: A:H.57, A:E.78, A:W.79, A:D.220, A:R.253, A:R.253, A:E.279, A:E.279 GYZ.23: 12 residues within 4Å: Chain B: H.57, E.78, W.79, H.126, H.127, Y.169, W.218, D.220, R.253, E.279, W.307 Ligands: SO4.26 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.218, B:E.279 Hydrogen bonds: B:H.57, B:W.79, B:Y.169, B:D.220, B:R.253, B:E.279

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

SO4.13: 3 residues within 4Å: Chain A: K.81, S.82, W.175 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.81, A:K.81, A:K.81, A:W.175, A:Y.182 Salt bridges: A:K.81 SO4.14: 2 residues within 4Å: Chain A: P.134, R.210 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.210 SO4.15: 6 residues within 4Å: Chain A: Y.317, E.323, R.327 Chain B: T.436, E.440, N.442 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.442 Water bridges: A:E.323, A:E.323, A:E.323, A:R.327 Salt bridges: A:R.327 SO4.16: 5 residues within 4Å: Chain A: R.253, R.262, H.263 Ligands: EDO.10, GYZ.12 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.253, A:R.262, A:H.263 SO4.24: 2 residues within 4Å: Chain B: K.363, R.367 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.452 Salt bridges: B:K.363, B:R.367 SO4.25: 7 residues within 4Å: Chain A: T.436, E.440, N.442 Chain B: Y.317, K.319, E.323, R.327 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.323, A:T.436, A:N.442 Water bridges: B:R.327, B:R.327 Salt bridges: B:R.327 SO4.26: 4 residues within 4Å: Chain B: R.253, R.262, H.263 Ligands: GYZ.23 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.253, B:R.262, B:H.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coyle, T. et al., Synthetic and Crystallographic Insight into Exploiting sp2Hybridization in the Development of alpha-l-Fucosidase Inhibitors. Chembiochem (2019)

Release Date

2019-02-20

Peptides

Alpha-L-fucosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-L-fucosidase