SMTL ID : 4ci9.1

Crystal structure of cathepsin A, apo-structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.79 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 DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: P.88, Y.89, L.439, F.442 No protein-ligand interaction detected (PLIP) DMS.11: 4 residues within 4Å: Chain B: P.88, Y.89, L.439, F.442 No protein-ligand interaction detected (PLIP)

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: Y.185, R.346, R.349 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.349 ACT.5: 7 residues within 4Å: Chain A: N.57, G.58, G.59, C.62, E.151, S.152, H.431 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.57, A:G.58, A:E.151 Water bridges: A:S.152 Salt bridges: A:H.431 ACT.12: 3 residues within 4Å: Chain B: Y.185, R.346, R.349 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.349 ACT.13: 7 residues within 4Å: Chain B: N.57, G.58, G.59, C.62, E.151, S.152, H.431 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.57, B:G.58 Water bridges: B:S.152 Salt bridges: B:H.431

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: N.247, Y.249, N.250, G.430, H.431, M.432, D.436 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.247, A:Y.249, A:N.250, A:M.432, A:D.436 Water bridges: A:D.436 GOL.7: 7 residues within 4Å: Chain A: S.184, E.186, Q.187, S.350, N.352, F.385, S.388 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.184, A:E.186, A:E.186, A:Q.187, A:S.350, A:S.350, A:S.388, A:S.388 Water bridges: A:Y.185 GOL.14: 7 residues within 4Å: Chain B: N.247, Y.249, N.250, G.430, H.431, M.432, D.436 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.247, B:Y.249, B:N.250, B:M.432, B:D.436 GOL.15: 7 residues within 4Å: Chain B: S.184, E.186, Q.187, S.350, N.352, F.385, S.388 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.184, B:E.186, B:Q.187, B:S.350, B:S.350, B:S.388, B:S.388 Water bridges: B:Y.185

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

SO4.8: 6 residues within 4Å: Chain A: Q.396, R.397, K.416 Chain B: G.203, R.205, L.206 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.397, B:G.203, B:G.203, B:R.205, B:L.206 Water bridges: A:V.395, A:K.416, A:K.416, B:N.204 Salt bridges: A:K.416 SO4.16: 6 residues within 4Å: Chain A: G.203, R.205, L.206 Chain B: Q.396, R.397, K.416 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.397, A:G.203, A:G.203, A:R.205, A:L.206 Water bridges: B:E.394, B:K.416, B:K.416, A:N.204 Salt bridges: B:K.416

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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