SMTL ID : 5eo8.1

Crystal structure of AOL(868)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

12 x TFU: methyl 1-seleno-beta-L-fucopyranoside(Non-covalent)

TFU.1: 11 residues within 4Å: Chain A: N.22, L.24, Y.40, W.44, W.271, R.277, Y.279, E.291, T.293, G.303, R.304 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.22, A:L.24, A:Y.40, A:W.271 Hydrogen bonds: A:W.44, A:R.277, A:R.277 TFU.2: 8 residues within 4Å: Chain A: R.25, Y.27, E.37, L.39, L.69, I.72, Y.88, W.94 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.69, A:I.72, A:Y.88 Hydrogen bonds: A:R.25, A:R.25, A:W.94 Water bridges: A:E.37, A:E.37 TFU.3: 13 residues within 4Å: Chain A: R.73, Y.75, E.85, A.87, Y.95, G.97, A.98, L.99, F.116, L.123, L.125, W.141, W.146 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.125, A:W.141 Hydrogen bonds: A:R.73, A:R.73, A:A.98, A:L.99, A:W.146 TFU.4: 12 residues within 4Å: Chain A: L.117, R.126, Y.128, E.138, M.140, N.142, G.149, T.150, P.174, I.176, Y.192, W.198 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.192 Hydrogen bonds: A:R.126, A:R.126, A:T.150, A:T.150, A:T.150, A:W.198 TFU.5: 13 residues within 4Å: Chain A: W.166, Y.168, R.177, Q.189, A.191, D.193, Y.199, E.201, T.203, I.227, M.229, W.245, Y.251 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.227, A:W.245 Hydrogen bonds: A:R.177, A:R.177, A:Q.189, A:E.201 Water bridges: A:T.203, A:T.203 TFU.6: 11 residues within 4Å: Chain A: F.220, R.230, Y.232, Q.242, C.244, R.255, I.257, P.274, L.276, W.292, W.294 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.220, A:P.274, A:L.276, A:W.294 Hydrogen bonds: A:R.230, A:R.230, A:Q.242, A:R.255 Water bridges: A:W.294, A:W.294 TFU.7: 11 residues within 4Å: Chain B: N.22, L.24, Y.40, W.44, W.271, R.277, Y.279, E.291, T.293, G.303, R.304 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.22, B:L.24, B:Y.40, B:W.271 Hydrogen bonds: B:W.44, B:R.277, B:R.277 TFU.8: 8 residues within 4Å: Chain B: R.25, Y.27, E.37, L.39, L.69, I.72, Y.88, W.94 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.69, B:I.72, B:Y.88 Hydrogen bonds: B:R.25, B:R.25, B:W.94 Water bridges: B:E.37 TFU.9: 13 residues within 4Å: Chain B: R.73, Y.75, E.85, A.87, Y.95, G.97, A.98, L.99, F.116, L.123, L.125, W.141, W.146 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.125, B:W.141 Hydrogen bonds: B:R.73, B:R.73, B:A.98, B:L.99, B:W.146 TFU.10: 12 residues within 4Å: Chain B: L.117, R.126, Y.128, E.138, M.140, N.142, G.149, T.150, P.174, I.176, Y.192, W.198 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.192 Hydrogen bonds: B:R.126, B:R.126, B:T.150, B:T.150, B:T.150, B:W.198 TFU.11: 13 residues within 4Å: Chain B: W.166, Y.168, R.177, Q.189, A.191, D.193, Y.199, E.201, T.203, I.227, M.229, W.245, Y.251 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.227, B:W.245 Hydrogen bonds: B:R.177, B:R.177, B:Q.189, B:E.201 Water bridges: B:T.203, B:T.203 TFU.12: 11 residues within 4Å: Chain B: F.220, R.230, Y.232, Q.242, C.244, R.255, I.257, P.274, L.276, W.292, W.294 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.220, B:P.274, B:L.276, B:W.294 Hydrogen bonds: B:R.230, B:R.230, B:Q.242, B:R.255 Water bridges: B:W.294, B:W.294

Links

RCSB   PDBe   PDBe-KB   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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