Research workbench
TMEM106B(120-254) singlet amyloid fibril from frontotemporal lobar degeneration with tdp-43 pathology (ftld-tdp) type a (case 2)
Analyse TMEM106B(120-254) singlet amyloid fibril from frontotemporal lobar degeneration… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U12
- Type
- protein
- Length
- 405 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane protein 106B
- UniProt
- Q9NUM4
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.55
Structure
electron microscopy · 1 distinct chain · 0% helix, 73% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Transmembrane protein 106B | protein | 135 | 0% helix, 73% strand | Q9NUM4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.55 | 0.78 | 24 | empty |
| 2 | 176 | 0.53 | 0.78 | 26 | empty |
| 3 | 244 | 0.51 | 0.74 | 24 | empty |
| 4 | 196 | 0.50 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6006 Ų buried · 193 hydrogen bonds · protein-protein
- A–B · 6005 Ų buried · 195 hydrogen bonds · protein-protein
- A–C · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 7U12 · TMEM106B(120-254) singlet amyloid fibril from frontotemporal lobar degeneration with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NUM4 · AlphaFold monomer V2.0 prediction for transmembrane protein 106B (Q9NUM4) · a predicted model of the same protein · chain A against A, TM-score 0.19
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 Q9NUM4
- Elsewhere: RCSB PDB 7U12 · PDBe 7U12 · UniProt Q9NUM4
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