MolNFT v1 · #180357 · protein

Tdp-43 lcd amyloid fibrils

7KWZ · Isoform 2 of tar DNA-binding protein 43: “Tdp-43 lcd amyloid fibrils”. Electron microscopy, 2 pockets (best druggability 0.56). MolNFT v1 #180357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KWZ
Type: protein
Length: 695 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isoform 2 of tar DNA-binding protein 43
UniProt: Q13148
Pockets: 2 · best druggability 0.56

Structure

electron microscopy · 1 distinct chain · 0% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Isoform 2 of tar DNA-binding protein 43	protein	139	0% helix, 35% strand	Q13148

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	108	0.56	0.84	25	empty
2	172	0.51	0.78	30	empty

Interfaces

9 interfaces between chains.

C–D · 5279 Å² buried · 176 hydrogen bonds · protein-protein
D–E · 5267 Å² buried · 176 hydrogen bonds · protein-protein
B–C · 5266 Å² buried · 175 hydrogen bonds · protein-protein
A–B · 5258 Å² buried · 173 hydrogen bonds · protein-protein
B–D · 399 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7KWZ · TDP-43 LCD amyloid fibrils · the same entry in another collection · chain B against B, TM-score 1.00
Q13148 · AlphaFold monomer V2.0 prediction for tar DNA-binding protein 43 (Q13148) · a predicted model of the same protein · chain A against A, TM-score 0.26

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 Q13148
Elsewhere: RCSB PDB 7KWZ · PDBe 7KWZ · UniProt Q13148

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