Research workbench
Structural basis for CSPG4 as a receptor for tcdb and a therapeutic target in clostridioides difficile infection
Analyse Structural basis for CSPG4 as a receptor for tcdb and a therapeutic target in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ML7
- Type
- protein
- Length
- 1,354 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B; Chondroitin sulfate proteoglycan 4
- EC
- 3.4.22.-
- UniProt
- P18177, Q6UVK1
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin B (EC 3.4.22.-) | protein | 1216 | 37% helix, 18% strand | P18177 |
| B | Chondroitin sulfate proteoglycan 4 | protein | 138 | 11% helix, 30% strand | Q6UVK1 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.84 | 0.85 | 145 | empty |
| 2 | 629 | 0.80 | 0.85 | 84 | empty |
| 3 | 710 | 0.78 | 0.82 | 62 | empty |
| 4 | 220 | 0.70 | 0.87 | 23 | empty |
| 5 | 362 | 0.65 | 0.80 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 1425 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7ML7 · Structural basis for CSPG4 as a receptor for TcdB and a therapeutic target in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6UVK1 · AlphaFold monomer V2.0 prediction for chondroitin sulfate proteoglycan 4 (Q6UVK1) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P18177
- Every structure of UniProt Q6UVK1
- Elsewhere: RCSB PDB 7ML7 · PDBe 7ML7 · UniProt P18177 · UniProt Q6UVK1
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