SMTL ID : 6str.1

Three dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with N,N'-Diacetylchitobiose; 60 seconds soaking

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 8 residues within 4Å: Chain A: D.87, S.106, W.108, F.110, E.116, F.117 Chain B: S.72, E.73 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:E.116, A:F.117 Hydrogen bonds: A:D.87, A:S.106, B:S.72, B:S.72, B:E.73, B:E.73 Water bridges: B:R.85, B:R.85 NAG.3: 7 residues within 4Å: Chain A: G.157, D.158 Chain B: S.20, Y.22, Y.24, A.30, Y.31 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.30, B:Y.31 Hydrogen bonds: B:S.20, B:Y.31, A:G.157, A:D.158 NAG.4: 8 residues within 4Å: Chain A: S.72, E.73 Chain B: D.87, S.106, W.108, F.110, E.116, F.117 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.117 Hydrogen bonds: B:D.87, B:S.106, B:F.110, A:S.72, A:S.72, A:E.73, A:E.73 Water bridges: A:R.85, A:R.85

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: L.89, C.90, W.108, G.109, F.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.90, A:G.109 Water bridges: A:C.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perduca, M. et al., Three-dimensional structure and properties of the giant reed (Arundo donax) lectin (ADL). Glycobiology (2021)

Release Date

2021-07-14

Peptides

Arundo donax Lectin (ADL): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Arundo donax Lectin (ADL)

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