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ALZHEIMER'S amyloid-beta peptide fragment 29-40 in complex with CD- substituted thermolysin

Analyse ALZHEIMER'S amyloid-beta peptide fragment 29-40 in complex with CD- substituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ONQ
Type: protein
Length: 321 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thermolysin; Amyloid-beta A4 protein
EC: 3.4.24.27
UniProt: P43133
Ligands: CD, CA

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thermolysin (EC 3.4.24.27)	protein	316	42% helix, 18% strand	P43133
B	Amyloid-beta A4 protein	protein	5	0% helix, 0% strand	—

Ligands and binding sites

CD · Cadmium ion · metal · 4 copies · chains A, B
CA · Calcium ion · metal · chains A
DMS · Dimethyl sulfoxide · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

A–B · 387 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5ONQ · Alzheimer's Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd-substituted Thermolysin · the same entry in another collection · chain A against A, TM-score 1.00
P43133 · AlphaFold monomer V2.0 prediction for thermolysin (P43133) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P43133
Elsewhere: RCSB PDB 5ONQ · PDBe 5ONQ · UniProt P43133

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