SMTL ID : 2fuq.1

Crystal Structure of Heparinase II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 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: 9 residues within 4Å: Chain A: F.72, Y.73, K.77, G.78, L.79, T.80, T.109, T.114 Ligands: FMT.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.72, A:Y.73 Hydrogen bonds: A:L.79, A:T.80, A:T.80, A:T.80 Water bridges: A:D.58, A:K.77 MAN-GCU-XYS-RAM.2: 7 residues within 4Å: Chain B: F.72, Y.73, K.77, G.78, L.79, T.80, T.109 6 PLIP interactions: 6 interactions with chain B Water bridges: B:T.112, B:T.112, B:T.112, B:K.77 Hydrophobic interactions: B:F.72, B:Y.73 Hydrogen bonds: B:L.79, B:T.80, B:T.80

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.383, D.400, F.420, H.426 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.383, A:D.400, A:H.426, H2O.15, H2O.15, H2O.16 ZN.7: 4 residues within 4Å: Chain B: H.383, D.400, F.420, H.426 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.383, B:D.400, B:H.426, H2O.32, H2O.33, H2O.33

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

PO4.4: 5 residues within 4Å: Chain A: L.585, P.586, N.590, D.640, Y.641 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.590, A:Y.641 Water bridges: A:D.587 PO4.8: 5 residues within 4Å: Chain B: L.585, P.586, N.590, D.640, Y.641 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.590, B:D.640, B:Y.641

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 3 residues within 4Å: Chain A: P.689, R.744, L.746 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.744 FMT.6: 3 residues within 4Å: Chain A: K.68, T.114 Ligands: MAN-GCU-XYS-RAM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.68, A:K.68 FMT.9: 3 residues within 4Å: Chain B: P.689, R.744, L.746 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.744

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