SMTL ID : 5la4.1

Crystal structure of apo human proheparanase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: Q.164, N.204, Q.207 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.2: 5 residues within 4Å: Chain A: K.396, H.424, N.425, V.426, K.428 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.396, A:N.425, A:K.396, A:H.424, A:K.428 Hydrophobic interactions: A:V.426

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

NAG.3: 3 residues within 4Å: Chain A: I.69, N.128, L.158 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: T.160, N.166, S.168 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.160 Hydrogen bonds: A:N.166, A:S.168

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

EDO.5: 7 residues within 4Å: Chain A: S.19, P.20, F.22, F.376, V.380, G.381, T.382 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.20, A:L.23, A:N.405 EDO.6: 6 residues within 4Å: Chain A: H.121, Y.264, Y.314, G.315, G.316, Y.357 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.315, A:G.316, A:Y.357 Water bridges: A:H.121 EDO.7: 6 residues within 4Å: Chain A: Y.140, N.144, L.148, D.149, L.150, N.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.150 EDO.8: 6 residues within 4Å: Chain A: Y.230, D.257, S.258, K.304, W.306, E.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.230, A:E.344 EDO.9: 2 residues within 4Å: Chain A: D.280, I.284 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.280, A:D.280

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Heparanase

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