SMTL ID : 8ohq.1

Crystal structure of human heparanase in complex with competitive inhibitor derrived from siastatin B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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: 5 residues within 4Å: Chain A: H.300, N.301, V.302, K.304 Chain B: D.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.300, A:K.304, A:K.304, A:N.301 Water bridges: A:H.300

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

NAG.2: 4 residues within 4Å: Chain A: F.2, N.4, L.33, L.34 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: T.36, N.42, S.44 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.36 Hydrogen bonds: A:N.42, A:S.44 NAG.4: 3 residues within 4Å: Chain A: D.25, N.59, F.100 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.100 Hydrogen bonds: A:D.25, A:N.59 Water bridges: A:N.59 NAG.5: 2 residues within 4Å: Chain A: N.80, Q.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80

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

EDO.6: 6 residues within 4Å: Chain A: G.257, T.258, T.280, N.281, T.282, D.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.258, A:T.280, A:T.282 EDO.11: 3 residues within 4Å: Chain A: R.216 Chain B: L.14, H.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.216, A:R.216, B:H.15 EDO.12: 5 residues within 4Å: Chain A: C.21, Q.348 Chain B: P.43, R.46, R.50 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:C.21, A:Q.348, B:P.43, B:R.46, B:R.50

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

CL.7: 3 residues within 4Å: Chain A: G.111, Q.112, H.138 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: G.229, A.230 Chain B: D.27 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: N.80, G.81, M.120, S.123 Ligand excluded by PLIP

1 x VGO: (3~{S},4~{S})-4,5,5-tris(oxidanyl)piperidine-3-carboxylic acid

VGO.10: 12 residues within 4Å: Chain A: N.66, E.67, Y.140, E.185, Y.190, G.191, G.192, Q.225, Y.233 Chain B: D.27, G.61, T.62 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.140, A:Y.140, A:E.185, A:G.191, A:G.192, B:T.62, B:T.62, B:T.62 Water bridges: B:T.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Molecular Basis for Inhibition of Heparanases and beta-Glucuronidases by Siastatin B. J.Am.Chem.Soc. (2024)

Release Date

2024-01-10

Peptides

Heparanase 50 kDa subunit: A
Heparanase 8 kDa subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Heparanase 50 kDa subunit

Heparanase 8 kDa subunit

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