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Crystal structure of the catalytic domain of lethal toxin from clostridium sordellii in complex with udp, castanospermine and calcium ion
Analyse Crystal structure of the catalytic domain of lethal toxin from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VL8
- Type
- protein
- Length
- 1,609 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytotoxin L
- UniProt
- Q46342
- Ligands
- UDP, CTS, CA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytotoxin L | protein | 539 | 56% helix, 8% strand | Q46342 |
| B | Cytotoxin L | protein | 533 | 57% helix, 8% strand | Q46342 |
| C | Cytotoxin L | protein | 537 | 57% helix, 7% strand | Q46342 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- CTS · Castanospermine · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.73 | 0.80 | 68 | empty |
| 2 | 1009 | 0.71 | 0.75 | 77 | empty |
| 3 | 611 | 0.69 | 0.78 | 51 | UDP, CTS, CA |
| 4 | 767 | 0.68 | 0.75 | 75 | UDP, CTS, CA |
| 5 | 677 | 0.65 | 0.75 | 54 | UDP, CTS, CA |
Interfaces
3 interfaces between chains.
- B–C · 553 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 329 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 317 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2VL8 · Crystal structure of the catalytic domain of lethal toxin from clostridium sordellii in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q46342 · AlphaFold monomer V2.0 prediction for cytotoxin-L (Q46342) · a predicted model of the same protein · chain B 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 Q46342
- Elsewhere: RCSB PDB 2VL8 · PDBe 2VL8 · UniProt Q46342
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