SMTL ID : 6zdm.1

Crystal structure of human heparanase in complex with a N',6O'-bis-sulfated 4-methylumbelliferyl heparan sulfate disaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.305, V.306 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.306

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

EDO.2: 1 residues within 4Å: Chain A: N.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.84

1 x QG2: (2~{S},3~{S},4~{R},5~{R},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-4,5-bis(oxidanyl)-3-(sulfoamino)-6-(sulfooxymethyl)oxan-2-yl]oxy-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid(Non-covalent)

QG2.3: 23 residues within 4Å: Chain A: K.5, F.6, N.70, E.71, Q.116, R.118, R.119, H.142, Y.144, 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 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.194, A:Y.194 Hydrogen bonds: A:N.70, A:E.71, A:G.195, A:G.196, A:Q.229, A:A.234, A:G.235, A:Y.237, A:Y.237, B:N.32, B:T.65, B:T.65 Water bridges: A:R.119, B:D.30, B:K.66 Salt bridges: A:K.5, A:R.119 pi-Stacking: A:Y.194 pi-Cation interactions: A:R.119

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

SO4.4: 7 residues within 4Å: Chain A: H.96, R.100, A.107, K.108, L.109, V.135, D.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.109, A:V.135 Salt bridges: A:H.96 SO4.5: 6 residues within 4Å: Chain A: V.269, R.274, R.275, K.276, L.277, H.304 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.275, A:K.276, A:L.277 Water bridges: A:K.308 Salt bridges: A:H.304 SO4.6: 3 residues within 4Å: Chain A: D.160, V.161, I.164 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.158 SO4.7: 2 residues within 4Å: Chain A: R.220 Chain B: L.17 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.220, B:H.18 Salt bridges: A:R.220 SO4.8: 5 residues within 4Å: Chain A: K.276, H.304, N.305, V.306, K.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.305 Salt bridges: A:K.276, A:H.304, A:K.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, L. et al., Structural insights into heparanase activity using a fluorogenic heparan sulfate disaccharide. Chem.Commun.(Camb.) (2020)

Release Date

2020-10-21

Peptides

Heparanase: A
Heparanase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Heparanase

Heparanase

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