SMTL ID : 4az0.1

crystal structure of cathepsin a, complexed with 8a.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

hetero-2-2-mer

Ligands

4 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: N.119, E.122 Chain B: R.45, L.47 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: P.79, D.80, G.257 Chain B: N.7, T.9, A.10, T.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.79 NAG-NAG.10: 4 residues within 4Å: Chain C: N.119, E.122 Chain D: R.45, L.47 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain C: P.79, D.80, G.257 Chain D: N.7, T.9, A.10, T.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.79

2 x S61: (S)-3-{[1-(2-Fluoro-phenyl)-5-hydroxy-1H-pyrazole-3-carbonyl]-amino}-3-o-tolyl-propionic acid(Non-covalent)

S61.3: 16 residues within 4Å: Chain A: N.57, G.58, G.59, P.60, C.62, D.66, E.151, S.152, Y.249 Chain B: P.3, M.35, C.36, N.37, F.38, N.41, H.131 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:D.66, A:Y.249, B:P.3, B:N.41 Hydrogen bonds: A:N.57, A:G.58, A:E.151, A:S.152, A:Y.249 Salt bridges: B:H.131 S61.12: 16 residues within 4Å: Chain C: N.57, G.58, G.59, P.60, C.62, D.66, E.151, S.152, Y.249 Chain D: P.3, M.35, C.36, N.37, F.38, N.41, H.131 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:D.66, C:Y.249, D:P.3, D:N.41 Hydrogen bonds: C:N.57, C:G.58, C:S.152 Salt bridges: D:H.131

12 x CD: CADMIUM ION(Non-covalent)

CD.4: 2 residues within 4Å: Chain A: E.186 Ligands: CD.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.186, H2O.6, H2O.8 CD.5: 2 residues within 4Å: Chain A: H.213, D.227 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.227, A:D.227 CD.6: 2 residues within 4Å: Chain A: D.224 Ligands: CD.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.224, A:D.224, H2O.6, H2O.8 CD.7: 1 residues within 4Å: Chain A: E.85 No protein-ligand interaction detected (PLIP) CD.8: 2 residues within 4Å: Chain A: N.250 Chain B: D.136 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.136, H2O.7 CD.9: 1 residues within 4Å: Chain B: C.36 No protein-ligand interaction detected (PLIP) CD.13: 2 residues within 4Å: Chain C: E.186 Ligands: CD.15 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.186, H2O.17, H2O.19 CD.14: 2 residues within 4Å: Chain C: H.213, D.227 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.227, C:D.227 CD.15: 2 residues within 4Å: Chain C: D.224 Ligands: CD.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.224, C:D.224, H2O.17, H2O.19 CD.16: 1 residues within 4Å: Chain C: E.85 No protein-ligand interaction detected (PLIP) CD.17: 2 residues within 4Å: Chain C: N.250 Chain D: D.136 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.136, H2O.19 CD.18: 1 residues within 4Å: Chain D: C.36 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruf, S. et al., Novel Beta-Amino Acid Derivatives as Inhibitors of Cathepsin A. J.Med.Chem. (2012)

Release Date

2012-09-26

Peptides

LYSOSOMAL PROTECTIVE PROTEIN 32 KDA CHAIN: AC
LYSOSOMAL PROTECTIVE PROTEIN 20 KDA CHAIN: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

LYSOSOMAL PROTECTIVE PROTEIN 32 KDA CHAIN

LYSOSOMAL PROTECTIVE PROTEIN 20 KDA CHAIN

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