Research workbench
Crystal structure of myotoxin II from bothrops moojeni complexed to caprylic acid
Analyse Crystal structure of myotoxin II from bothrops moojeni complexed to caprylic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B81
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic phospholipase A2 homolog 2
- UniProt
- Q9I834
- Ligands
- OCA, SO4
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Basic phospholipase A2 homolog 2 | protein | 122 | 48% helix, 7% strand | Q9I834 |
Ligands and binding sites
- OCA · Octanoic acid (caprylic acid) · ligand · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 6 copies · chains B, A
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 | 658 | 0.80 | 0.84 | 72 | OCA |
Interfaces
1 interface between chains.
- B–A · 991 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6B81 · Crystal structure of Myotoxin II from Bothrops moojeni complexed to Caprylic acid · the same entry in another collection · chain B against B, TM-score 1.00
- Q9I834 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog myotoxin II (Q9I834) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9I834
- Elsewhere: RCSB PDB 6B81 · PDBe 6B81 · UniProt Q9I834
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