SMTL ID : 2vuz.1

Crystal structure of Codakine in complex with biantennary nonasaccharide at 1.7A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-NAG-MAN-NAG.1: 14 residues within 4Å: Chain A: S.61, F.62, P.91, E.93, N.95, S.97, E.101, N.107, W.108, N.112, D.113, L.114, R.115 Ligands: CA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.107, A:E.93, A:N.95, A:E.101, A:N.112, A:R.115, A:P.91, A:N.95, A:S.97 Water bridges: A:R.115

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.93, N.95, E.101, N.112, D.113 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.93, A:E.101, A:D.113, A:D.113

3 x GOL: GLYCEROL(Non-covalent)

GOL.3: 7 residues within 4Å: Chain A: E.39, D.41, W.77, S.79, S.80, A.82, Q.125 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.79, A:S.80, A:Q.125 Water bridges: A:D.41, A:W.77 GOL.4: 4 residues within 4Å: Chain A: W.75, A.83, F.84, L.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.75, A:F.84, A:F.84 GOL.5: 5 residues within 4Å: Chain A: Q.27, Q.31, I.36, S.78, S.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.27, A:Q.31

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Gourdine, J.P. et al., High Affinity Interaction between a Bivalve C-Type Lectin and a Biantennary Complex-Type N-Glycan Revealed by Crystallography and Microcalorimetry. J.Biol.Chem. (2008)

Release Date

2008-08-05

Peptides

CODAKINE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CODAKINE

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