SMTL ID : 5eo7.1 (1 other biounit)

Crystal structure of AOL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

10 x SFU: methyl 1-seleno-alpha-L-fucopyranoside(Non-covalent)

SFU.1: 9 residues within 4Å: Chain A: R.24, Y.26, E.36, L.38, N.45, L.68, I.71, Y.87, W.93 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.71 Hydrogen bonds: A:R.24, A:R.24, A:E.36, A:W.93 SFU.2: 14 residues within 4Å: Chain A: R.72, Y.74, E.84, A.86, D.88, Y.94, G.96, A.97, L.98, F.115, L.122, L.124, W.140, W.145 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.122, A:L.124 Hydrogen bonds: A:R.72, A:R.72, A:E.84, A:A.97, A:L.98, A:W.145 SFU.3: 11 residues within 4Å: Chain A: L.116, R.125, Y.127, E.137, M.139, N.141, T.149, P.173, I.175, Y.191, W.197 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.175, A:Y.191 Hydrogen bonds: A:R.125, A:R.125, A:E.137, A:T.149, A:T.149, A:W.197 SFU.4: 13 residues within 4Å: Chain A: F.219, R.229, Y.231, Q.241, C.243, D.252, R.254, I.256, P.273, L.275, W.291, W.293 Ligands: SO4.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.219, A:P.273 Hydrogen bonds: A:R.229, A:R.229, A:Q.241 Water bridges: A:D.252 SFU.5: 12 residues within 4Å: Chain A: N.21, L.23, Y.39, W.43, W.270, R.276, Y.278, E.290, T.292, G.302, R.303 Ligands: SO4.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.21, A:L.23, A:Y.39 Hydrogen bonds: A:W.43, A:R.276, A:R.276, A:E.290 SFU.9: 9 residues within 4Å: Chain B: R.24, Y.26, E.36, L.38, N.45, L.68, I.71, Y.87, W.93 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.71 Hydrogen bonds: B:R.24, B:R.24, B:E.36, B:W.93 SFU.10: 14 residues within 4Å: Chain B: R.72, Y.74, E.84, A.86, D.88, Y.94, G.96, A.97, L.98, F.115, L.122, L.124, W.140, W.145 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.122, B:L.124 Hydrogen bonds: B:R.72, B:R.72, B:E.84, B:A.97, B:L.98, B:W.145 SFU.11: 11 residues within 4Å: Chain B: L.116, R.125, Y.127, E.137, M.139, N.141, T.149, P.173, I.175, Y.191, W.197 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.175, B:Y.191 Hydrogen bonds: B:R.125, B:R.125, B:E.137, B:T.149, B:T.149, B:W.197 SFU.12: 13 residues within 4Å: Chain B: F.219, R.229, Y.231, Q.241, C.243, D.252, R.254, I.256, P.273, L.275, W.291, W.293 Ligands: SO4.16 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.219, B:P.273 Hydrogen bonds: B:R.229, B:R.229, B:Q.241 Water bridges: B:D.252, B:D.252 SFU.13: 12 residues within 4Å: Chain B: N.21, L.23, Y.39, W.43, W.270, R.276, Y.278, E.290, T.292, G.302, R.303 Ligands: SO4.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.21, B:L.23, B:Y.39 Hydrogen bonds: B:W.43, B:R.276, B:R.276, B:E.290

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

SO4.6: 5 residues within 4Å: Chain A: Y.39, G.42, W.43, R.303 Ligands: SFU.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.43 Salt bridges: A:R.303 SO4.7: 2 residues within 4Å: Chain A: K.185, T.203 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.203, A:T.203 Water bridges: A:K.185, A:T.203 Salt bridges: A:K.185 SO4.8: 4 residues within 4Å: Chain A: W.293, G.298, S.299 Ligands: SFU.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.293, A:S.299 SO4.14: 5 residues within 4Å: Chain B: Y.39, G.42, W.43, R.303 Ligands: SFU.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.43 Salt bridges: B:R.303 SO4.15: 2 residues within 4Å: Chain B: K.185, T.203 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.203, B:T.203 Water bridges: B:K.185, B:T.203 Salt bridges: B:K.185 SO4.16: 4 residues within 4Å: Chain B: W.293, G.298, S.299 Ligands: SFU.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.293, B:S.299

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Makyio, H. et al., Six independent fucose-binding sites in the crystal structure of Aspergillus oryzae lectin. Biochem.Biophys.Res.Commun. (2016)

Release Date

2016-06-29

Peptides

Predicted protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Predicted protein

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