SMTL ID : 6wia.1

CRYSTAL STRUCTURE OF HUMAN PROTECTIVE PROTEIN/CATHEPSIN A, DFP-INHIBITED (AGED)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 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.117, T.119, E.120, R.343, L.345 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: P.77, D.78, G.255, N.305, T.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.77 NAG-NAG.15: 5 residues within 4Å: Chain B: N.117, T.119, E.120, R.343, L.345 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain B: P.77, D.78, G.255, N.305, T.307 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.77

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

ACT.3: 7 residues within 4Å: Chain A: N.55, G.56, G.57, C.60, E.149, S.150, H.429 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.55, A:G.56, A:E.149 Salt bridges: A:H.429 ACT.4: 4 residues within 4Å: Chain A: L.180, Y.183, N.186, D.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.186 ACT.5: 4 residues within 4Å: Chain A: L.354, L.357, S.358, Q.389 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.389 ACT.6: 3 residues within 4Å: Chain A: Q.363, M.391, H.418 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.363, A:Q.363, A:H.418 Salt bridges: A:H.418, A:K.449 ACT.7: 6 residues within 4Å: Chain A: Y.247, N.248, G.428, H.429, M.430, D.434 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.248, A:H.429, A:M.430 ACT.17: 7 residues within 4Å: Chain B: N.55, G.56, G.57, C.60, E.149, S.150, H.429 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.55, B:G.56 Salt bridges: B:H.429 ACT.18: 4 residues within 4Å: Chain B: L.180, Y.183, N.186, D.187 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.186 ACT.19: 4 residues within 4Å: Chain B: L.354, L.357, S.358, Q.389 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.389 ACT.20: 3 residues within 4Å: Chain B: Q.363, M.391, H.418 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.363, B:Q.363, B:H.418 Salt bridges: B:H.418, B:K.449 ACT.21: 6 residues within 4Å: Chain B: Y.247, N.248, G.428, H.429, M.430, D.434 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.248, B:H.429, B:M.430

12 x CD: CADMIUM ION(Non-covalent)

CD.8: 2 residues within 4Å: Chain A: H.33, D.110 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.33, A:D.110, A:D.110 CD.9: 3 residues within 4Å: Chain A: Q.130, D.166, S.168 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.166, A:D.166, A:S.168, H2O.6, H2O.6 CD.10: 2 residues within 4Å: Chain A: H.211, D.225 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.211, A:D.225, A:D.225 CD.11: 2 residues within 4Å: Chain A: E.184 Ligands: CD.12 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.184, H2O.2, H2O.6 CD.12: 2 residues within 4Å: Chain A: D.222 Ligands: CD.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.222, A:D.222, H2O.6 CD.13: 1 residues within 4Å: Chain A: E.415 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.415, A:E.415 CD.22: 2 residues within 4Å: Chain B: H.33, D.110 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.33, B:D.110, B:D.110 CD.23: 3 residues within 4Å: Chain B: Q.130, D.166, S.168 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.166, B:D.166, B:S.168, H2O.13, H2O.13 CD.24: 2 residues within 4Å: Chain B: H.211, D.225 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.211, B:D.225, B:D.225 CD.25: 2 residues within 4Å: Chain B: E.184 Ligands: CD.26 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.184, H2O.9, H2O.12 CD.26: 2 residues within 4Å: Chain B: D.222 Ligands: CD.25 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.222, B:D.222, H2O.12 CD.27: 1 residues within 4Å: Chain B: E.415 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.415, B:E.415

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 9 residues within 4Å: Chain A: Y.402, Q.408, I.409, A.410, K.425, K.435 Chain B: Y.250, A.251, P.252 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.402, A:K.425, A:K.435, B:Y.250 GOL.28: 9 residues within 4Å: Chain A: Y.250, A.251, P.252 Chain B: Y.402, Q.408, I.409, A.410, K.425, K.435 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.425, B:K.435, A:Y.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bouknight, K.D. et al., Structural and kinetic evidence of aging after organophosphate inhibition of human Cathepsin A. Biochem. Pharmacol. (2020)

Release Date

2020-04-29

Peptides

Lysosomal protective protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lysosomal protective protein