MolNFT v1 · #187360 · protein
Cryo-EM structure of TMEM106B fibrils extracted from a ftld-tdp patient, polymorph 1
7SAQ · Transmembrane protein 106B: “Cryo-EM structure of TMEM106B fibrils extracted from a ftld-tdp patient, polymorph 1”. Electron microscopy, 1 ligand (NAG), 7 pockets (best druggability 0.77). MolNFT v1 #187360 on GenesisL1: 3D…
- PDB
- 7SAQ
- Type
- protein
- Length
- 675 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane protein 106B
- UniProt
- Q9NUM4
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 0% helix, 82% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Transmembrane protein 106B | protein | 135 | 0% helix, 82% strand | Q9NUM4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, D, E, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.77 | 0.84 | 36 | empty |
| 2 | 679 | 0.75 | 0.81 | 49 | empty |
| 3 | 322 | 0.75 | 0.87 | 37 | empty |
| 4 | 880 | 0.72 | 0.76 | 65 | empty |
| 5 | 123 | 0.67 | 0.90 | 29 | empty |
Interfaces
7 interfaces between chains.
- A–D · 5947 Ų buried · 200 hydrogen bonds · protein-protein
- B–C · 5944 Ų buried · 198 hydrogen bonds · protein-protein
- C–D · 5942 Ų buried · 198 hydrogen bonds · protein-protein
- A–E · 5939 Ų buried · 197 hydrogen bonds · protein-protein
- B–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SAQ · Cryo-EM structure of TMEM106B fibrils extracted from a FTLD-TDP patient, polymorph 1 · 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 0.20
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 7SAQ · PDBe 7SAQ · UniProt Q9NUM4
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