SMTL ID : 5bwi.1

Crystallographic structure of a bacterial heparanase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: R.25, A.27, R.28, D.29, A.61 Chain B: D.355 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.25, A:R.25, A:R.28 Water bridges: A:D.29, B:D.355 GOL.2: 5 residues within 4Å: Chain A: Y.42, E.83, T.84, S.85, T.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.85 Water bridges: A:T.310

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

ACT.3: 8 residues within 4Å: Chain A: R.216, M.226, L.227, S.228, P.229, D.230, W.276, N.279 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.230, A:W.276

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: N.57, G.60, C.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.57 Water bridges: A:N.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bohlmann, L. et al., Functional and structural characterization of a heparanase. Nat.Chem.Biol. (2015)

Release Date

2015-10-28

Peptides

Glycoside Hydrolase Family 79: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycoside Hydrolase Family 79