SMTL ID : 3e80.1 (2 other biounits)

Structure of Heparinase II complexed with heparan sulfate degradation disaccharide product

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x MAN- GCU- XYS- RAM: alpha-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose

MAN-GCU-XYS-RAM.1: 7 residues within 4Å: Chain A: F.74, Y.75, K.79, G.80, L.81, T.82, T.111 7 PLIP interactions: 7 interactions with chain A Water bridges: A:T.116, A:D.60 Hydrophobic interactions: A:F.74, A:Y.75 Hydrogen bonds: A:K.79, A:L.81, A:T.82, A:T.82

1 x NDG- GCD: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG-GCD.2: 16 residues within 4Å: Chain A: D.122, R.125, K.174, G.178, H.179, E.182, Y.234, R.238, N.382, H.383, Y.406, Y.413, N.414, G.446, G.447 Ligands: PO4.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.234, A:Y.406, A:R.238, A:N.382, A:N.382, A:Y.413, A:N.414, A:G.447 Salt bridges: A:R.125, A:H.179, A:R.238, A:H.383, A:H.179 Hydrophobic interactions: A:K.174

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.385, D.402, H.428 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.385, A:D.402, A:H.428, H2O.1, H2O.1, H2O.8

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 6 residues within 4Å: Chain A: F.72, R.73, D.122, R.125, Y.234 Ligands: NDG-GCD.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.122, A:Y.234 Water bridges: A:R.125 Salt bridges: A:R.73, A:R.125 PO4.5: 5 residues within 4Å: Chain A: G.411, G.412, Y.413, N.414, S.415 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.412, A:N.414, A:N.414 Water bridges: A:Y.413 PO4.6: 4 residues within 4Å: Chain A: K.657, H.659, E.660, A.675 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.660, A:A.675 Salt bridges: A:K.657, A:H.659 PO4.7: 5 residues within 4Å: Chain A: L.587, P.588, N.592, D.642, Y.643 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.592, A:D.642, A:D.642, A:Y.643, A:Y.643 Water bridges: A:D.589

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaya, D. et al., Catalytic mechanism of heparinase II investigated by site-directed mutagenesis and the crystal structure with its substrate. J.Biol.Chem. (2010)

Release Date

2008-12-30

Peptides

Heparinase II protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Heparinase II protein

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