MolNFT v1 · #27905 · protein
Structural insights for fatty acid binding in a LYS49 phospholipase A2: crystal structure of myotoxin II from bothrops moojeni complexed with stearic acid
1XXS · Phospholipase A2 homolog 2: “Structural insights for fatty acid binding in a LYS49 phospholipase A2: crystal structure of myotoxin II from…”. X-ray diffraction, 2 ligands (STE, SO4), 3 pockets (best druggability 0.56). MolNFT v1…
- PDB
- 1XXS
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 homolog 2
- EC
- 3.1.1.4
- UniProt
- Q9I834
- Ligands
- STE, SO4
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 homolog 2 (EC 3.1.1.4) | protein | 122 | 48% helix, 8% strand | Q9I834 |
Ligands and binding sites
- STE · Stearic acid · ligand · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.56 | 0.84 | 19 | STE |
| 2 | 130 | 0.48 | 0.78 | 21 | STE |
| 3 | 90 | 0.38 | 0.76 | 10 | STE |
Interfaces
1 interface between chains.
- A–B · 396 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1XXS · Structural insights for fatty acid binding in a Lys49 phospholipase A2: crystal structure… · the same entry in another collection · chain A against A, 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 A 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 1XXS · PDBe 1XXS · UniProt Q9I834
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