MolNFT v1 · #37621 · protein
Clostridium difficile toxin a fragment bound to AGAL(1,3)BGAL(1,4) bglcnac
2G7C: “Clostridium difficile toxin a fragment bound to AGAL(1,3)BGAL(1,4) bglcnac”. X-ray diffraction, 3 ligands (NAG, GAL, GLA), 2 pockets (best druggability 0.67). MolNFT v1 #37621 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2G7C
- Type
- protein
- Length
- 499 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin a
- UniProt
- P16154
- Ligands
- NAG, GAL, GLA
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin a | protein | 245 | 0% helix, 50% strand | P16154 |
| B | Toxin a | protein | 254 | 0% helix, 49% strand | P16154 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.67 | 0.76 | 66 | GAL, GLA |
| 2 | 207 | 0.56 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 806 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2G7C · Clostridium difficile Toxin A Fragment Bound to aGal(1,3)bGal(1,4)bGlcNAc · the same entry in another collection · chain A against A, TM-score 1.00
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 P16154
- Elsewhere: RCSB PDB 2G7C · PDBe 2G7C · UniProt P16154
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