SMTL ID : 7yke.1

Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 4,6-sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

2 x 8EX- GCD: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4,6-di-O-sulfo-beta-D-galactopyranose(Non-covalent)

8EX-GCD.1: 7 residues within 4Å: Chain A: D.490, R.500, H.501, Y.508, R.560, Y.655, T.713 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.500, A:H.501, A:Y.655, A:Y.655, A:Y.655, A:T.713, A:Y.508, A:Y.655 Water bridges: A:E.502, A:R.500, A:R.560, A:R.560, A:R.560 Salt bridges: A:R.500, A:H.501, A:H.501, A:R.500, A:H.501 8EX-GCD.2: 12 residues within 4Å: Chain A: T.275, N.276, R.395, N.447, T.448, 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:T.275, A:N.276, A:N.447, A:G.507, A:R.560, A:N.564 Water bridges: A:R.560, A:H.561, A:H.561 Salt bridges: A:R.395

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: H.43, M.70, 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

Watanabe, I. et al., Biochemical and crystallographic assessments of the effect of 4,6-O-disulfated disaccharide moieties in chondroitin sulfate E on chondroitinase ABC I activity. Febs J. (2023)

Release Date

2022-11-30

Peptides

Chondroitin sulfate ABC endolyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Chondroitin sulfate ABC endolyase

Related Entries With Identical Sequence