Research workbench
X-ray structure of crotamine, a cell-penetrating peptide from the brazilian snake crotalus durissus terrificus
Analyse X-ray structure of crotamine, a cell-penetrating peptide from the brazilian… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GV5
- Type
- protein
- Length
- 126 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crotamine ile-19
- UniProt
- P01475
- Ligands
- SCN, SO4
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Crotamine ile-19 | protein | 42 | 19% helix, 26% strand | P01475 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 4 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains B, A, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.49 | 0.81 | 19 | SCN, SO4 |
| 2 | 163 | 0.48 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 382 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 137 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4GV5 · X-ray structure of crotamine, a cell-penetrating peptide from the Brazilian snake… · 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 P01475
- Elsewhere: RCSB PDB 4GV5 · PDBe 4GV5 · UniProt P01475
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