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Crystal structure of the catalytic domain of lethal toxin from clostridium sordellii in complex with udp-glc and manganese 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
- 2VKD
- Type
- protein
- Length
- 1,621 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytotoxin L
- UniProt
- Q46342
- Ligands
- UPG, MN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytotoxin L | protein | 542 | 58% helix, 7% strand | Q46342 |
| B | Cytotoxin L | protein | 538 | 57% helix, 8% strand | Q46342 |
| C | Cytotoxin L | protein | 541 | 56% helix, 7% strand | Q46342 |
Ligands and binding sites
- UPG · Uridine-5'-diphosphate-glucose · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) 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 | 679 | 0.76 | 0.81 | 61 | MN, UPG |
| 2 | 789 | 0.76 | 0.80 | 79 | MN, UPG |
| 3 | 668 | 0.74 | 0.80 | 64 | MN, UPG |
| 4 | 440 | 0.70 | 0.81 | 49 | empty |
| 5 | 600 | 0.68 | 0.78 | 61 | empty |
Interfaces
3 interfaces between chains.
- B–C · 562 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 365 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2VKD · 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 2VKD · PDBe 2VKD · UniProt Q46342
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