SMTL ID : 3imn.1

Crystal structure of heparin lyase I from Bacteroides thetaiotaomicron

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: Q.22, H.151, P.154, R.156, Q.223, G.224 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.22, A:Q.223, A:G.224 Water bridges: A:R.156, A:R.156 Salt bridges: A:H.151, A:R.156 SO4.2: 3 residues within 4Å: Chain A: R.27, I.28, S.93 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.28, A:S.93 Water bridges: A:N.29, A:S.93 SO4.3: 2 residues within 4Å: Chain A: D.140, S.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.140, A:S.141, A:S.141 SO4.4: 3 residues within 4Å: Chain A: Y.226, R.255, N.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.257 Salt bridges: A:R.255 SO4.5: 2 residues within 4Å: Chain A: K.97, G.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.98 Water bridges: A:K.97 Salt bridges: A:K.97 SO4.6: 1 residues within 4Å: Chain A: R.62 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.62

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: D.155, E.222, W.248, N.345, D.346 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.222, A:W.248, A:N.345, A:D.346, H2O.10

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

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