SMTL ID : 6ljl.1

Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasaccharide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x SGN- IDS- SGN- GCD: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose

SGN-IDS-SGN-GCD.1: 28 residues within 4Å: Chain A: L.69, D.70, G.71, S.226, R.230, R.233, R.332, A.334, D.335, N.336, H.337, Q.340, M.341, A.389, H.392, V.393, S.442, Q.446, E.489, K.491, P.492, S.554, R.579, G.581, F.582, R.648, K.755, R.757 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.442, A:Q.446, A:R.579, A:S.226, A:Q.340, A:Q.340, A:R.579, A:R.233, A:E.489, A:R.757 Water bridges: A:E.489, A:R.757, A:R.757, A:R.757, A:D.70, A:N.336, A:R.579, A:F.582, A:R.230, A:R.230, A:R.233, A:R.233 Salt bridges: A:R.757, A:R.579, A:R.579, A:K.755, A:R.230, A:R.233, A:K.755, A:R.757

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: Q.340, W.384, N.386, A.390, N.394 No protein-ligand interaction detected (PLIP) CA.3: 6 residues within 4Å: Chain A: H.439, G.440, R.546, A.556, L.557, N.559 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Q. et al., Discovery of exolytic heparinases and their catalytic mechanism and potential application. Nat Commun (2021)

Release Date

2020-12-23

Peptides

Heparinase II/III-like protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Heparinase II/III-like protein