SMTL ID : 3ilr.1

Structure of Heparinase I from Bacteroides thetaiotaomicron in complex with tetrasaccharide product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x IXD- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(4-1)-4-deoxy-2-O-sulfo-beta-D-erythro-hex-4-enopyranuronic acid(Non-covalent)

IXD-SGN.1: 19 residues within 4Å: Chain A: G.68, Y.69, E.73, T.74, K.75, I.140, G.218, G.219, Y.220, P.221, K.235, K.246, R.249, N.251, Y.351, V.353, G.354, D.355 Ligands: SGN-IXD.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.69, A:E.73, A:Y.220, A:R.249, A:N.251, A:G.354, A:D.355, A:G.219, A:G.219, A:R.249, A:N.251, A:N.251 Salt bridges: A:R.249, A:K.75, A:K.235, A:K.246, A:R.249 Water bridges: A:Y.220, A:K.235, A:R.249

1 x SGN- IXD: 4-deoxy-2-O-sulfo-beta-D-erythro-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose(Non-covalent)

SGN-IXD.2: 15 residues within 4Å: Chain A: Q.16, V.33, K.75, R.77, E.79, Q.143, H.145, Q.217, G.218, G.219, P.221, Y.345, K.347, Y.351 Ligands: IXD-SGN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.77, A:R.77, A:Q.143, A:Q.217, A:G.218, A:Q.16, A:Q.217, A:G.218, A:Y.345, A:Y.345 Water bridges: A:G.146, A:Q.217 Salt bridges: A:K.75, A:R.77, A:H.145, A:K.347, A:R.77, A:K.105, A:K.347

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.216, W.242, R.338, N.339, D.340 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:W.242, A:N.339, A:D.340, H2O.1, H2O.1

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: N.180, T.244, D.245, K.246, D.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.180, A:T.244, A:K.246 EDO.5: 3 residues within 4Å: Chain A: D.166, E.167, E.170 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.170 EDO.6: 3 residues within 4Å: Chain A: Q.4, T.5, F.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.4, A:F.45 EDO.7: 4 residues within 4Å: Chain A: P.195, K.197, P.203, Y.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.205, A:Y.205 EDO.8: 4 residues within 4Å: Chain A: D.18, R.21, Y.98, Q.102 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.21, A:R.21, A:Y.98, A:Y.98, A:Q.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, Y.H. et al., Structural snapshots of heparin depolymerization by heparin lyase I. J.Biol.Chem. (2009)

Release Date

2009-09-29

Peptides

Heparin lyase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Heparin lyase I