SMTL ID : 4cib.1

crystal structure of cathepsin a, complexed with compound 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

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: 5 residues within 4Å: Chain A: N.119, T.121, E.122, R.345, L.347 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: P.79, D.80, G.257, N.307, T.309, A.310, T.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.79 Water bridges: A:T.313 NAG-NAG.9: 5 residues within 4Å: Chain B: N.119, T.121, E.122, R.345, L.347 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain B: P.79, D.80, G.257, N.307, T.309, A.310, T.313 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.79

2 x 7UZ: 2-(cyclohexylmethyl)propanedioic acid(Non-covalent)

7UZ.3: 10 residues within 4Å: Chain A: N.57, G.58, G.59, C.62, D.66, E.151, S.152, Y.153, M.335, H.431 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.66 Hydrogen bonds: A:N.57, A:G.58, A:G.59, A:E.151, A:S.152, A:Y.153 Salt bridges: A:H.431, A:H.431 7UZ.11: 10 residues within 4Å: Chain B: N.57, G.58, G.59, C.62, D.66, E.151, S.152, Y.153, M.335, H.431 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:D.66 Hydrogen bonds: B:N.57, B:G.58, B:G.59, B:S.152, B:Y.153 Salt bridges: B:H.431, B:H.431

10 x CD: CADMIUM ION(Non-covalent)

CD.4: 2 residues within 4Å: Chain A: D.224 Ligands: CD.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.224, A:D.224, H2O.20, H2O.23, H2O.23 CD.5: 5 residues within 4Å: Chain A: G.181, L.182, C.377, D.382 Ligands: CD.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.181, A:D.382, H2O.20, H2O.20 CD.6: 2 residues within 4Å: Chain A: E.186 Ligands: CD.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.186, H2O.20, H2O.20, H2O.23, H2O.34 CD.7: 1 residues within 4Å: Chain A: D.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.5, A:D.5, H2O.34 CD.8: 5 residues within 4Å: Chain A: L.182, N.188, A.376, C.377 Ligands: CD.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.377 CD.12: 2 residues within 4Å: Chain B: D.224 Ligands: CD.14 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.224, B:D.224, H2O.55, H2O.58, H2O.58 CD.13: 5 residues within 4Å: Chain B: G.181, L.182, C.377, D.382 Ligands: CD.16 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.181, B:D.382, H2O.55, H2O.55 CD.14: 2 residues within 4Å: Chain B: E.186 Ligands: CD.12 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.186, H2O.55, H2O.55, H2O.58, H2O.69 CD.15: 1 residues within 4Å: Chain B: D.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.5, B:D.5, H2O.69 CD.16: 5 residues within 4Å: Chain B: L.182, N.188, A.376, C.377 Ligands: CD.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schreuder, H.A. et al., Crystal structure of cathepsin A, a novel target for the treatment of cardiovascular diseases. Biochem. Biophys. Res. Commun. (2014)

Release Date

2014-02-26

Peptides

LYSOSOMAL PROTECTIVE PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

LYSOSOMAL PROTECTIVE PROTEIN

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