SMTL ID : 5e9b.1

Crystal structure of human heparanase in complex with HepMer M09S05a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-mer

Ligands

1 x BDP- SGN- BDP- GNS: 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid

BDP-SGN-BDP-GNS.1: 22 residues within 4Å: Chain A: K.5, F.6, N.70, E.71, H.142, Y.144, R.149, E.189, Y.194, G.195, G.196, Q.229, V.230, G.233, A.234, G.235, Y.237 Chain B: D.30, N.32, G.64, T.65, K.66 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.149, B:N.32, A:Q.229, A:A.234, A:G.235, A:Y.237 Salt bridges: A:R.149, A:K.5 Water bridges: B:D.30, B:D.30, B:T.65

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: T.40, A.41, N.46, S.48 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.40 Hydrogen bonds: A:N.46, A:S.48 NAG.3: 5 residues within 4Å: Chain A: D.42, L.43, N.84, S.86, Q.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.84 NAG.4: 2 residues within 4Å: Chain A: N.305, V.306 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: G.261, T.262, N.285, T.286 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, L. et al., Structural characterization of human heparanase reveals insights into substrate recognition. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-11-18

Peptides

Heparanase: A
Heparanase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heparanase

Heparanase

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