SMTL ID : 6czs.1

Crystal structure of human pro-cathepsin H C26S mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

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.1: 10 residues within 4Å: Chain A: K.106, S.107, N.108, F.176, N.177, S.187, Q.188, E.191, Y.195, N.230 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.175, A:D.175 Hydrophobic interactions: A:Q.188

2 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.2: 2 residues within 4Å: Chain A: Q.182, D.211 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.211 GLC-GLC.3: 2 residues within 4Å: Chain A: Y.234, N.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.320 Water bridges: A:K.319

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

NAG.4: 5 residues within 4Å: Chain A: E.98, P.99, N.101, N.177, H.179 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.177 Water bridges: A:N.177, A:H.179, A:Q.188

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

SO4.5: 3 residues within 4Å: Chain A: R.111, D.235, E.237 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.111, A:R.111, A:R.111, A:R.111, A:D.235, A:D.235 Salt bridges: A:R.111 SO4.6: 3 residues within 4Å: Chain A: R.111, T.113, G.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.114 Water bridges: A:R.111, A:R.111 Salt bridges: A:R.111 SO4.7: 2 residues within 4Å: Chain A: H.42, Q.81 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.44, A:K.44 Salt bridges: A:H.42, A:K.44 SO4.8: 3 residues within 4Å: Chain A: A.104, T.105, K.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.105, A:T.105, A:K.106 SO4.9: 2 residues within 4Å: Chain A: K.226, D.227 No protein-ligand interaction detected (PLIP)

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

CL.10: 1 residues within 4Å: Chain A: N.292 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: R.263, T.264 Ligand excluded by PLIP

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