SMTL ID : 8e08.1

Crystal structure of HPSE P6 in complex with tetraose pentosan inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-1-1-mer

Ligands

3 x XY6- XY6- XY6- XY9: 2,3,4-tri-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose

XY6-XY6-XY6-XY9.1: 8 residues within 4Å: Chain A: F.80, N.82, G.83, G.117, K.118, K.121, M.122, S.125 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.121, A:N.82, A:G.83, A:S.125 Salt bridges: A:K.118, A:K.121, A:K.121 Water bridges: A:S.84 XY6-XY6-XY6-XY9.2: 16 residues within 4Å: Chain A: K.3, K.5, K.76, G.194, Q.227, G.231, A.232, G.233, Y.235 Chain B: D.45, N.47, L.48, T.80, K.81 Ligands: ACT.4, SO4.7 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:K.3, A:K.5, A:K.5, A:K.76 XY6-XY6-XY6-XY9.3: 4 residues within 4Å: Chain A: E.152, D.158, K.274, N.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.152, A:R.272, A:N.303 Water bridges: A:N.156, A:K.274 Salt bridges: A:K.274, A:K.274

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 8 residues within 4Å: Chain A: Y.142, E.187, Y.192, G.193, G.194, Q.227, Y.235 Ligands: XY6-XY6-XY6-XY9.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.193, A:G.194 ACT.6: 1 residues within 4Å: Chain A: R.11 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.11

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 1 residues within 4Å: Chain A: R.74 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.74 SO4.7: 1 residues within 4Å: Ligands: XY6-XY6-XY6-XY9.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whitefield, C. et al., Complex Inhibitory Mechanism of Glycomimetics with Heparanase. Biochemistry (2023)

Release Date

2023-07-12

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heparanase 50 kDa subunit

Heparanase 8 kDa subunit

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