SMTL ID : 6lja.1

Crystal Structure of exoHep from Bacteroides intestinalis DSM 17393 complexed with disaccharide product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x SGN- UAP: 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose(Non-covalent)

SGN-UAP.1: 18 residues within 4Å: Chain A: L.69, D.70, G.71, S.226, F.282, R.332, A.334, D.335, N.336, H.337, Q.340, Y.390, S.554, H.555, R.579, G.581, F.582, R.648 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.70, A:G.71, A:V.72, A:D.335, A:D.335, A:N.336, A:N.336, A:S.226, A:Q.340, A:Y.390, A:R.579 Water bridges: A:D.70, A:R.332, A:R.332, A:R.332, A:R.332, A:R.332, A:H.337, A:H.337, A:H.337, A:R.648, A:R.648, A:R.648, A:D.70 Salt bridges: A:R.332, A:H.337, A:R.648, A:H.337, A:H.555, A:R.579

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: Q.340, W.384, N.386, Y.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