SMTL ID : 5l9y.1

Crystal structure of human heparanase, in complex with glucuronic acid configured aziridine probe JJB355

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain A: H.304, N.305, V.306, K.308 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.304, A:K.308, B:D.5 Water bridges: A:N.305

2 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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.40 Hydrogen bonds: A:N.46, A:S.48 NAG.3: 2 residues within 4Å: Chain A: N.84, Q.87 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.84, A:N.84

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

EDO.4: 5 residues within 4Å: Chain A: F.256, V.260, G.261, T.262 Chain B: S.21 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: D.163, I.166, R.274, R.275, R.278 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: D.241, D.245, P.246, L.247, K.337, S.338 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.246

1 x 6S6: (1~{S},2~{R},3~{S},4~{S},5~{S},6~{R})-2-(8-azidooctylamino)-3,4,5,6-tetrakis(oxidanyl)cyclohexane-1-carboxylic acid(Covalent)

6S6.7: 13 residues within 4Å: Chain A: N.70, E.71, R.118, Y.144, E.189, Y.194, G.195, G.196, Q.229, Y.237 Chain B: D.30, G.64, T.65 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.144, A:E.189, A:Y.194, A:Y.194 Hydrogen bonds: A:N.70, A:N.70, A:E.71, A:G.195, A:G.196, A:Q.229, A:Y.237, B:D.30, B:T.65, B:T.65 Water bridges: A:R.118, A:R.118, B:K.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, L. et al., Activity-based probes for functional interrogation of retaining beta-glucuronidases. Nat. Chem. Biol. (2017)

Release Date

2017-05-31

Peptides

Heparanase: A
Heparanase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heparanase

Heparanase

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