SMTL ID : 6czk.1

Crystal structure of wild-type human pro-cathepsin H

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: P.99, N.101, N.177, H.179 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 8 residues within 4Å: Chain A: N.108, F.176, N.177, S.187, Q.188, E.191, Y.195, N.230 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.188

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

SO4.3: 3 residues within 4Å: Chain A: R.111, D.235, E.237 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.111, A:R.111, A:R.111, A:R.111, A:R.111, A:D.235, A:D.235 Salt bridges: A:R.111 SO4.4: 3 residues within 4Å: Chain A: R.111, T.113, G.114 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.114 Water bridges: A:R.111, A:R.111, A:G.112, A:T.113 Salt bridges: A:R.111 SO4.5: 4 residues within 4Å: Chain A: H.42, R.43, Q.81 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.42, A:R.43 SO4.6: 2 residues within 4Å: Chain A: K.226, D.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.227 Salt bridges: A:K.226

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: K.133, N.134, E.202, Y.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.134, A:N.134 Water bridges: A:Y.207 GOL.8: 6 residues within 4Å: Chain A: Y.116, P.117, P.118, E.237, V.240, R.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.237, A:R.317, A:R.317 GOL.9: 7 residues within 4Å: Chain A: Q.81, F.82, Y.94, N.134, G.136, A.137 Ligands: SO4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hao, Y. et al., Crystal structures of human procathepsin H. PLoS ONE (2018)

Release Date

2018-08-08

Peptides

Pro-cathepsin H: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pro-cathepsin H