SMTL ID : 3nbe.1

Clitocybe nebularis ricin B-like lectin (CNL) in complex with N,N'-diacetyllactosediamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x Z3Q- NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-2-azidoethyl 2-acetamido-2-deoxy-beta-D-glucopyranoside(Non-covalent)(Non-functional Binders)

Z3Q-NGA.1: 11 residues within 4Å: Chain A: D.20, L.21, T.22, G.23, S.24, I.33, H.35, N.38, Y.44, N.46, S.123 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.44 Hydrogen bonds: A:D.20, A:G.23, A:N.38, A:N.46, A:N.46, A:Q.47, A:S.123, A:S.123 Water bridges: A:S.24 Z3Q-NGA.2: 12 residues within 4Å: Chain B: D.20, L.21, T.22, G.23, S.24, I.33, H.35, N.38, Y.44, N.46, Q.47, S.123 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.44 Hydrogen bonds: B:D.20, B:G.23, B:N.38, B:N.46, B:Q.47 Water bridges: B:G.23, B:G.23

2 x SO4: SULFATE ION(Non-covalent)(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: N.16, R.17, D.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.16 Salt bridges: A:R.17 SO4.4: 3 residues within 4Å: Chain B: N.16, R.17, H.36 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.16 Salt bridges: B:R.17

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Pohleven, J. et al., Bivalent carbohydrate binding is required for biological activity of Clitocybe nebularis lectin (CNL), the N,N'-diacetyllactosediamine (GalNAc beta 1-4GlcNAc, LacdiNAc)-specific lectin from basidiomycete C. nebularis. J.Biol.Chem. (2012)

Release Date

2011-07-13

Peptides

Ricin B-like lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ricin B-like lectin

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