Research workbench
Cryoem structure of the C. sordellii lethal toxin tcsl in complex with SEMA6A
Analyse Cryoem structure of the C. sordellii lethal toxin tcsl in complex with SEMA6A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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