SMTL ID : 5e97.1

Glycoside Hydrolase ligand structure 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

hetero-1-1-mer

Ligands

1 x BDP- NDG- BDP- NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid

BDP-NDG-BDP-NDG.1: 17 residues within 4Å: Chain A: N.70, Y.144, R.149, E.189, Y.194, G.195, G.196, Q.229, V.230, A.234, G.235, Y.237 Chain B: D.30, N.32, G.64, T.65 Ligands: NPO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.149, A:G.235 Water bridges: A:G.196

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

NAG.2: 2 residues within 4Å: Chain A: F.6, N.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.8 Water bridges: A:N.35 NAG.3: 3 residues within 4Å: Chain A: T.40, N.46, S.48 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.40 Hydrogen bonds: A:S.48 NAG.4: 2 residues within 4Å: Chain A: N.84, Q.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.84 NAG.5: 1 residues within 4Å: Chain A: N.305 No protein-ligand interaction detected (PLIP)

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

CL.6: 5 residues within 4Å: Chain A: F.82, N.84, G.85, M.124, S.127 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: K.276, H.304 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: E.71, G.115, Q.116, H.142 Ligands: NPO.9 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: R.49 Ligand excluded by PLIP

1 x NPO: P-NITROPHENOL(Non-covalent)

NPO.9: 6 residues within 4Å: Chain A: E.71, Q.116, Y.144, Y.194 Ligands: BDP-NDG-BDP-NDG.1, CL.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.144, A:Y.144, A:Y.194 Water bridges: A:N.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, L. et al., Structural characterization of human heparanase reveals insights into substrate recognition. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-11-18

Peptides

Heparanase: A
Heparanase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heparanase

Heparanase

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