SMTL ID : 3e7j.1

HeparinaseII H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x NAG- GCU- NAG- GCD: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GCU-NAG-GCD.1: 17 residues within 4Å: Chain A: F.72, R.73, D.122, R.125, K.174, G.178, S.233, N.382, H.383, Y.406, Y.413, N.414, G.446, G.447, S.448, I.468 Ligands: ACT.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.73, A:S.233, A:Y.406, A:R.73, A:R.73, A:R.125, A:R.125 Water bridges: A:S.233, A:S.233, A:D.122, A:D.122, A:R.125, A:D.122, A:R.125 Salt bridges: A:R.73, A:H.383 NAG-GCU-NAG-GCD.2: 16 residues within 4Å: Chain B: F.72, R.73, D.122, R.125, K.174, V.177, G.178, N.382, H.383, Y.406, Y.413, N.414, G.446, G.447, S.448, I.468 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.73, B:Y.406, B:R.73, B:R.73, B:R.125, B:R.125 Salt bridges: B:R.73, B:H.383 Hydrophobic interactions: B:F.72

2 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.15, H2O.16 ZN.8: 4 residues within 4Å: Chain B: H.385, D.402, F.422, H.428 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.385, B:D.402, B:H.428, H2O.27, H2O.28, H2O.30

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 6 residues within 4Å: Chain A: W.61, F.74, Y.75, N.77, Q.78, K.79 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.75, A:Q.78 Hydrogen bonds: A:N.77, A:K.79 ACT.5: 5 residues within 4Å: Chain A: K.550, P.635, K.636, K.637, A.638 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.637 Water bridges: A:K.550 ACT.6: 1 residues within 4Å: Chain A: K.485 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.482 ACT.7: 4 residues within 4Å: Chain A: Y.406, Y.413 Ligands: NAG-GCU-NAG-GCD.1, NAG-GCU-NAG-GCD.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.413 Hydrogen bonds: A:Y.406 ACT.9: 4 residues within 4Å: Chain B: W.247, D.250, R.251, Y.305 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.251

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heparinase II protein