SMTL ID : 5e98.1

Crystal structure of human heparanase in complex with HepMer M04S02a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

hetero-1-1-mer

Ligands

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

BDP-GNS-BDP.1: 22 residues within 4Å: Chain A: K.5, F.6, N.70, E.71, Y.144, R.149, E.189, Y.194, G.195, G.196, G.197, Q.229, V.230, G.233, A.234, G.235, Y.237 Chain B: D.30, N.32, G.64, T.65 Ligands: NPO.7 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.149, A:R.149, A:Q.229, A:A.234, A:G.235, B:D.30, B:N.32 Water bridges: B:D.30, B:D.30, B:T.65

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 4 residues within 4Å: Chain A: F.173, M.221, G.222 Chain B: H.18 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.18

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

NAG.3: 3 residues within 4Å: Chain A: T.40, 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.4: 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.5: 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.6: 3 residues within 4Å: Chain A: E.134, R.180, K.183 Ligand excluded by PLIP

1 x NPO: P-NITROPHENOL(Non-covalent)

NPO.7: 6 residues within 4Å: Chain A: E.71, Q.116, Y.144, Y.194 Chain B: T.65 Ligands: BDP-GNS-BDP.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.144, A:Y.144, A:Y.194 Water bridges: A:N.70

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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