MolNFT v1 · #188625 · protein
TMEM106B(120-254) T185S singlet amyloid fibril from frontotemporal lobar degeneration with tdp-43 pathology (ftld-tdp) type B case 2 (case 7).
7U17 · Transmembrane protein 106B: “TMEM106B(120-254) T185S singlet amyloid fibril from frontotemporal lobar degeneration with tdp-43 pathology…”. Electron microscopy, 1 ligand (NAG), 2 pockets (best druggability 0.54). MolNFT v1 #188625…
- PDB
- 7U17
- 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
- 2 · best druggability 0.54
Structure
electron microscopy · 1 distinct chain · 0% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Transmembrane protein 106B | protein | 135 | 0% helix, 35% strand | Q9NUM4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.54 | 0.76 | 28 | empty |
| 2 | 53 | 0.41 | 0.82 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6260 Ų buried · 166 hydrogen bonds · protein-protein
- B–A · 6250 Ų buried · 163 hydrogen bonds · protein-protein
- A–C · 388 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 7U17 · TMEM106B(120-254) T185S singlet amyloid fibril from frontotemporal lobar degeneration… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NUM4 · AlphaFold monomer V2.0 prediction for transmembrane protein 106B (Q9NUM4) · a predicted model of the same protein · chain B against A, TM-score 0.18
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 7U17 · PDBe 7U17 · UniProt Q9NUM4
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