SMTL ID : 5la7.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 6 residues within 4Å: Chain A: K.393, K.396, H.424, N.425, V.426, K.428 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.426 Hydrogen bonds: A:K.393, A:H.424, A:K.428 Water bridges: A:K.428

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

NAG.2: 3 residues within 4Å: Chain A: F.126, N.128, L.158 No protein-ligand interaction detected (PLIP) NAG.3: 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 NAG.4: 2 residues within 4Å: Chain A: N.204, Q.207 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.204

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

EDO.5: 7 residues within 4Å: Chain A: S.19, F.22, F.376, V.380, G.381, T.382 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: P.20, K.377, V.380, T.382, N.405 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.377 Water bridges: A:K.377 EDO.7: 7 residues within 4Å: Chain A: L.464, T.465, L.466, P.475, P.476, L.477, M.478 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.478 EDO.8: 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.9: 5 residues within 4Å: Chain A: F.293, E.297, P.301, G.302, K.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.297, A:G.302, A:K.303 EDO.10: 3 residues within 4Å: Chain A: T.33, D.34, Q.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.113, A:Q.113

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)

6S6.11: 13 residues within 4Å: Chain A: D.28, G.62, T.63, H.121, N.190, E.191, Y.264, E.309, Y.314, G.315, G.316, Q.349, Y.357 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:E.309, A:Y.314, A:Y.314 Hydrogen bonds: A:D.28, A:T.63, A:T.63, A:N.190, A:N.190, A:E.191, A:G.315, A:G.316, A:Q.349, A:Y.357 Water bridges: A:N.30, A:N.30, A:N.30, A:Y.357 Salt bridges: A:H.121

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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