MolNFT v1 · #43783 · protein

40-residue D23N beta amyloid fibril

2LNQ · P3(40): “40-residue D23N beta amyloid fibril”. Solid-state nmr, 4 pockets (best druggability 0.69). MolNFT v1 #43783 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2LNQ
Type: protein
Length: 208 residues
Chains: 8
Method: solid-state nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P3(40)
UniProt: P05067
Pockets: 4 · best druggability 0.69

Structure

solid-state nmr · 1 distinct chain · 0% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	P3(40)	protein	26	0% helix, 42% strand	P05067

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	64	0.69	0.96	24	empty
2	183	0.67	0.86	37	empty
3	77	0.59	0.89	24	empty
4	51	0.31	0.77	14	empty

Interfaces

12 interfaces between chains.

G–H · 1001 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 980 Å² buried · 31 hydrogen bonds · protein-protein
E–F · 943 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 919 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 807 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

2LNQ · 40-residue D23N beta amyloid fibril · the same entry in another collection · chain H against H, TM-score 1.00
P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain C against A, TM-score 0.35

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 P05067
Elsewhere: RCSB PDB 2LNQ · PDBe 2LNQ · UniProt P05067

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