Research workbench
Piratoxin-II (prtx-II) - a K49 PLA2 from bothrops pirajai
Analyse Piratoxin-II (prtx-II) - a K49 PLA2 from bothrops pirajai in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QLL
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P82287
- Ligands
- TDA
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 (EC 3.1.1.4) | protein | 121 | 49% helix, 5% strand | P82287 |
Ligands and binding sites
- TDA · N-tridecanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.54 | 0.81 | 22 | TDA |
| 2 | 125 | 0.51 | 0.80 | 23 | TDA |
Interfaces
1 interface between chains.
- A–B · 458 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1QLL · Piratoxin-II (Prtx-II) - a K49 PLA2 from Bothrops pirajai · the same entry in another collection · chain A against A, TM-score 1.00
- P82287 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog piratoxin-2 (P82287) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P82287
- Elsewhere: RCSB PDB 1QLL · PDBe 1QLL · UniProt P82287
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