Research workbench
X-ray structure at 1.55 a of toxin gamma, a cardiotoxin from naja nigricollis venom. crystal packing reveals a model for insertion into membranes
Analyse X-ray structure at 1.55 a of toxin gamma, a cardiotoxin from naja nigricollis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TGX
- Type
- protein
- Length
- 180 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-cardiotoxin
- UniProt
- P01468
- Ligands
- CL
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Gamma-cardiotoxin | protein | 60 | 0% helix, 42% strand | P01468 |
Ligands and binding sites
- CL · Chloride ion · ion · 14 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.81 | 0.83 | 90 | CL |
Interfaces
3 interfaces between chains.
- A–B · 522 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 266 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 240 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1TGX · X-ray structure at 1.55 a of toxin gamma, a cardiotoxin from naja nigricollis venom.… · the same entry in another collection · chain A against A, TM-score 1.00
- P01468 · AlphaFold monomer V2.0 prediction for cytotoxin 1 (P01468) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 P01468
- Elsewhere: RCSB PDB 1TGX · PDBe 1TGX · UniProt P01468
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