MolNFT v1 · #129553 · protein

ALZHEIMER'S amyloid-beta peptide fragment 1-40 in complex with thermolysin

5ONR: “ALZHEIMER'S amyloid-beta peptide fragment 1-40 in complex with thermolysin”. X-ray diffraction, 2 ligands (CA, ZN), 1 pocket (best druggability 0.31). MolNFT v1 #129553 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ONR
Type: protein
Length: 319 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: P00800
Ligands: CA, ZN
Pockets: 1 · best druggability 0.31

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	41% helix, 18% strand	P00800
B	Amyloid-beta A4 protein	protein	3	0% helix, 0% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A
ZN · Zinc ion · metal · chains A, B
DMS · Dimethyl sulfoxide · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.31	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 298 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5ONR · Alzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin · the same entry in another collection · 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 P00800
Elsewhere: RCSB PDB 5ONR · PDBe 5ONR · UniProt P00800

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