SMTL ID : 7eiq.1

Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 4S

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x ASG- GCD: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose(Non-covalent)

ASG-GCD.1: 6 residues within 4Å: Chain A: R.500, H.501, Y.508, R.560, Y.655, T.713 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.500, A:Y.655 Water bridges: A:R.560, A:R.560, A:R.560 Salt bridges: A:R.500, A:H.501 ASG-GCD.2: 9 residues within 4Å: Chain A: N.276, N.447, Y.505, G.507, Y.508, P.511, R.560, H.561, N.564 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.505, A:Y.508 Hydrogen bonds: A:N.276, A:N.276, A:N.447, A:G.507, A:R.560, A:R.560, A:H.561, A:N.564 Water bridges: A:N.564 ASG-GCD.3: 6 residues within 4Å: Chain A: K.710, H.712, T.713, L.714, M.715, R.966 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.715, A:M.715, A:T.713, A:T.713 Salt bridges: A:K.710, A:R.966 Water bridges: A:H.712

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: H.43, M.70, G.71, Q.73, D.211 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.43, A:M.70, A:Q.73, A:D.211, A:D.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takashima, M. et al., Substrate specificity of Chondroitinase ABC I based on analyses of biochemical reactions and crystal structures in complex with disaccharides. Glycobiology (2021)

Release Date

2021-08-25

Peptides

Chondroitin sulfate ABC endolyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Chondroitin sulfate ABC endolyase

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