SMTL ID : 5e9c.1

Crystal structure of human heparanase in complex with heparin tetrasaccharide dp4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 5KV- IDR- SGN- UAP: 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-beta-D-glucopyranose

5KV-IDR-SGN-UAP.1: 25 residues within 4Å: Chain A: K.5, F.6, N.70, E.71, G.115, Q.116, R.118, H.142, H.143, 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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.116, A:Q.116, A:Y.144, A:G.195, B:T.65, A:N.70, A:E.71, A:G.195, A:G.196, A:Q.229, A:Y.237, B:T.65, B:T.65, A:Q.229, A:A.234, A:G.235, A:Y.237, B:D.30, B:N.32, A:G.195, A:G.196 Water bridges: A:R.118, A:R.118, A:Y.194, A:Y.194, B:K.66, B:D.30, B:N.32 Salt bridges: A:R.118, A:R.149, A:K.5, A:R.149

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

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

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

CL.5: 1 residues within 4Å: Chain A: K.276 Ligand excluded by PLIP

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

SO4.6: 6 residues within 4Å: Chain A: D.245, P.246, W.251, K.347, M.348 Chain B: K.47 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.348 Water bridges: A:D.245, A:D.245 Salt bridges: A:K.347, B:K.47

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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