MolNFT v1 · #143724 · protein
Crystal structure of myotoxin II from bothrops moojeni complexed to caprylic acid
6B81 · Basic phospholipase A2 homolog 2: “Crystal structure of myotoxin II from bothrops moojeni complexed to caprylic acid”. X-ray diffraction, 2 ligands (OCA, SO4), 1 pocket (best druggability 0.80). MolNFT v1 #143724 on GenesisL1: 3D…
- 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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