SMTL ID : 8e07.1

Crystal structure of HPSE P6 in complex with triose pentosan inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

2 x 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

XY6-XY6-XY9.1: 12 residues within 4Å: Chain A: K.5, G.194, G.231, A.232, G.233, Y.235 Chain B: D.45, N.47, L.48, T.80, K.81 Ligands: ACT.3 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:T.80, B:K.81 Salt bridges: B:K.81, B:K.81, A:K.5, A:K.5 XY6-XY6-XY9.2: 7 residues within 4Å: Chain A: F.80, N.82, G.83, K.121, M.122, S.125 Ligands: NH4.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.121, A:N.82, A:G.83, A:S.125 Salt bridges: A:K.121, A:K.121

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

ACT.3: 8 residues within 4Å: Chain A: Y.142, E.187, Y.192, G.193, G.194, Q.227, Y.235 Ligands: XY6-XY6-XY9.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.193, A:G.194, A:Y.235, A:Y.235

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

SO4.4: 5 residues within 4Å: Chain A: G.231, H.236, D.239, E.240, N.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.240, A:N.241 Salt bridges: A:H.236 SO4.5: 4 residues within 4Å: Chain A: G.131, E.132, R.178, K.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.131 Salt bridges: A:R.178, A:K.181 SO4.7: 1 residues within 4Å: Chain A: Q.350 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.348, A:D.348, A:T.351 SO4.8: 4 residues within 4Å: Chain A: P.326, H.327, G.328, Q.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.328 Water bridges: A:P.326, A:G.328 SO4.9: 4 residues within 4Å: Chain A: R.272, K.274, H.302, N.303 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.303, A:N.303, A:N.303 Water bridges: A:K.274 Salt bridges: A:R.272, A:K.274, A:H.302

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.6: 5 residues within 4Å: Chain A: N.82, G.83, S.84, S.125 Ligands: XY6-XY6-XY9.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.83, A:S.84, A:S.125, A:S.125

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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