SMTL ID : 5onp.1

Alzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd-substituted Thermolysin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

monomer

Ligands

1 x GLY- ALA- ILE- ILE- GLY: Amyloid-beta A4 protein(Non-covalent)

GLY-ALA-ILE-ILE-GLY.1: 15 residues within 4Å: Chain A: Y.110, N.111, N.112, A.113, F.114, F.130, L.133, H.142, E.143, E.166, L.202, R.203, D.226, H.231 Ligands: CD.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.114, A:F.130, A:L.133, A:H.142, A:L.202, A:L.202 Hydrogen bonds: A:Y.110, A:N.112, A:N.112, A:N.112, A:A.113, A:R.203, A:R.203 Water bridges: A:Y.157, A:Y.157

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.177, N.183, D.185, E.190 Ligands: CA.3 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.177, A:N.183, A:D.185, A:E.190, H2O.3, H2O.4 CA.3: 6 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, E.190 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.138, A:E.177, A:E.177, A:D.185, A:E.190 CA.4: 4 residues within 4Å: Chain A: Y.193, T.194, I.197, D.200 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.193, A:I.197, A:D.200, H2O.4, H2O.11

2 x CD: CADMIUM ION(Non-covalent)

CD.5: 6 residues within 4Å: Chain A: H.142, E.143, H.146, E.166 Ligands: GLY-ALA-ILE-ILE-GLY.1, GLY-ALA-ILE-ILE-GLY.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.142, A:E.143, A:H.146, A:E.166 CD.6: 3 residues within 4Å: Chain A: D.57, D.59, Q.61 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.57, A:Q.61, H2O.3, H2O.4, H2O.12

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 1 residues within 4Å: Chain A: Y.66 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leite, J.P. et al., Alzheimer's A beta1-40peptide degradation by thermolysin: evidence of inhibition by a C-terminal A beta product. FEBS Lett. (2019)

Release Date

2018-08-29

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermolysin

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