MolNFT v1 · #168871 · protein
Cryoem structure of the C. sordellii lethal toxin tcsl in complex with SEMA6A
6WTS: “Cryoem structure of the C. sordellii lethal toxin tcsl in complex with SEMA6A”. Electron microscopy, 1 ligand (NAG), 14 pockets (best druggability 0.78). MolNFT v1 #168871 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6WTS
- Type
- protein
- Length
- 1,287 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SEMA6A; Tcsl
- EC
- 2.4.1.-
- UniProt
- Q9H2E6, V5T923
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SEMA6A | protein | 536 | 10% helix, 35% strand | Q9H2E6 |
| B | SEMA6A | protein | 532 | 9% helix, 37% strand | Q9H2E6 |
| C | Tcsl (EC 2.4.1.-) | protein | 219 | 16% helix, 46% strand | V5T923 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.78 | 0.80 | 104 | empty |
| 2 | 873 | 0.78 | 0.81 | 82 | empty |
| 3 | 837 | 0.78 | 0.81 | 77 | empty |
| 4 | 214 | 0.68 | 0.85 | 24 | empty |
| 5 | 166 | 0.58 | 0.81 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1082 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 700 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6WTS · CryoEM structure of the C. sordellii lethal toxin TcsL in complex with SEMA6A · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H2E6 · AlphaFold monomer V2.0 prediction for semaphorin-6A (Q9H2E6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9H2E6
- Every structure of UniProt V5T923
- Elsewhere: RCSB PDB 6WTS · PDBe 6WTS · UniProt Q9H2E6 · UniProt V5T923
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.