SMTL ID : 5l9z.1

Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted glucuronic acid configured aziridine probe JJB355

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: T.40, N.46, S.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.48 Water bridges: A:N.46, A:N.46 NAG.2: 2 residues within 4Å: Chain A: N.84, Q.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.84 NAG.3: 1 residues within 4Å: Chain A: N.305 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.305 Water bridges: A:K.276, A:H.304, A:H.304, A:N.305 NAG.4: 2 residues within 4Å: Chain A: N.63, F.104 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.104 Water bridges: A:N.63

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

EDO.5: 6 residues within 4Å: Chain A: G.261, T.262, T.284, N.285, T.286, D.287 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.262, A:T.286 Water bridges: A:T.262, A:T.284 EDO.6: 3 residues within 4Å: Chain A: F.173, M.221 Chain B: H.18 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.221 EDO.7: 4 residues within 4Å: Chain A: R.153, H.332, L.334, L.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.153, A:R.153, A:L.334 EDO.8: 1 residues within 4Å: Chain A: Q.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.170 EDO.9: 4 residues within 4Å: Chain A: K.323, L.325, N.342, K.360 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.323, A:G.343 EDO.10: 2 residues within 4Å: Chain A: P.199, L.200 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: C.25 Chain B: P.46, R.49, R.53 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:Q.352 Hydrogen bonds: B:R.49, B:R.53

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

CL.11: 2 residues within 4Å: Chain A: R.180, K.183 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: N.84, G.85, M.124, S.127 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: G.233, A.234 Chain B: L.33 Ligand excluded by PLIP

1 x GUX: (1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-[8-[(azanylidene-{4}-azanylidene)amino]octyl]-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid(Non-covalent)

GUX.14: 15 residues within 4Å: Chain A: N.70, E.71, Q.116, R.118, Y.144, Y.145, Q.189, Y.194, G.195, G.196, Q.229, Y.237 Chain B: D.30, G.64, T.65 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.194, A:Y.194, A:Y.194 Hydrogen bonds: A:N.70, A:E.71, A:Q.116, A:Y.145, A:Q.189, A:G.195, A:G.196, A:Q.229, B:T.65, B:T.65 Salt bridges: A:E.71 Water bridges: 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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