SMTL ID : 4p8w.1

The crystal structures of YKL-39 in the presence of chitooligosaccharides (GlcNAc4) were solved to resolutions of 1.9 angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

1 x NDG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-functional Binders)

NDG-NAG-NAG-NAG.1: 17 residues within 4Å: Chain A: Y.13, W.17, F.44, G.84, Y.85, L.86, S.124, I.126, Y.127, L.191, F.193, D.194, W.199, Y.250, F.282, W.341, M.345 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.17, A:Y.85 Water bridges: A:S.279

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

SO4.2: 3 residues within 4Å: Chain A: K.213, G.219, S.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.219, A:S.222 Water bridges: A:K.213 Salt bridges: A:K.213 SO4.3: 4 residues within 4Å: Chain A: D.97, S.98, S.99, R.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.99 Salt bridges: A:R.102 SO4.4: 1 residues within 4Å: Chain A: R.366 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.362 Salt bridges: A:R.366 SO4.5: 4 residues within 4Å: Chain A: F.87, G.88, S.89, K.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.89, A:S.89, A:K.90 Salt bridges: A:K.90 SO4.6: 4 residues within 4Å: Chain A: S.46, E.48, K.55, F.87 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.46, A:S.46 Water bridges: A:I.47 Salt bridges: A:K.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ranok, A. et al., Structural and Thermodynamic Insights into Chitooligosaccharide Binding to Human Cartilage Chitinase 3-like Protein 2 (CHI3L2 or YKL-39). J.Biol.Chem. (2015)

Release Date

2014-12-03

Peptides

Chitinase-3-like protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Chitinase-3-like protein 2

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