SMTL ID : 3ikw.1

Structure of Heparinase I from Bacteroides thetaiotaomicron

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.220, W.246, R.342, N.343, D.344 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:W.246, A:N.343, A:D.344, H2O.1, H2O.1

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: N.27, I.29 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.27 Water bridges: A:D.31, A:G.32, A:R.47 EDO.3: 5 residues within 4Å: Chain A: N.184, T.248, D.249, K.250, D.251 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.184, A:T.248, A:K.250 EDO.4: 4 residues within 4Å: Chain A: Q.158, T.159, G.216, L.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.158 EDO.5: 3 residues within 4Å: Chain A: S.135, S.136, L.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.137 Water bridges: A:L.137, A:S.139 EDO.6: 4 residues within 4Å: Chain A: L.156, V.164, W.246, E.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.164 EDO.7: 6 residues within 4Å: Chain A: R.244, S.269, E.270, Y.271, K.272, L.339 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, Y.H. et al., Structural snapshots of heparin depolymerization by heparin lyase I. J.Biol.Chem. (2009)

Release Date

2009-09-29

Peptides

Heparin lyase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Heparin lyase I