SMTL ID : 2fut.1

Crystal Structure of Heparinase II Complexed with a Disaccharide Product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 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: 19 residues within 4Å: Chain A: D.121, R.124, K.173, V.176, G.177, H.178, E.181, Y.233, R.237, N.381, H.382, Y.405, G.411, Y.412, N.413, G.445, G.446, S.447, I.467 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.381, A:N.381, A:N.381, A:N.381, A:N.413, A:G.446, A:G.446, A:Y.233, A:Y.405, A:Y.405, A:Y.405, A:Y.412 Water bridges: A:D.172, A:H.178, A:N.381, A:N.381, A:G.445, A:A.468, A:G.411 Salt bridges: A:H.178, A:R.124, A:H.178, A:R.237, A:H.382 SGN-UAP.2: 18 residues within 4Å: Chain B: D.121, R.124, V.176, G.177, H.178, E.181, Y.233, R.237, N.381, H.382, Y.405, G.411, Y.412, N.413, G.445, G.446, S.447, I.467 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.237, B:N.381, B:N.381, B:N.381, B:N.381, B:N.413, B:N.413, B:G.446, B:S.447, B:Y.405, B:Y.412 Water bridges: B:D.172, B:H.178, B:N.381, B:N.413, B:A.468, B:G.411 Salt bridges: B:H.178, B:R.124, B:H.178, B:R.237, B:H.382 Hydrophobic interactions: B:Y.233

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.384, D.401, F.421, H.427 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.384, A:D.401, A:H.427, H2O.4, H2O.12, H2O.19 ZN.4: 4 residues within 4Å: Chain B: H.384, D.401, F.421, H.427 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.384, B:H.427, H2O.25, H2O.29, H2O.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaya, D. et al., Crystal Structure of Heparinase II from Pedobacter heparinus and Its Complex with a Disaccharide Product. J.Biol.Chem. (2006)

Release Date

2006-04-18

Peptides

heparinase II protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

heparinase II protein