Research workbench
Crystal structure of a acidic PLA2 from trimeresurus stejnegeri venom
Analyse Crystal structure of a acidic PLA2 from trimeresurus stejnegeri venom in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RFP
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acidic phospholipase A2 5
- EC
- 3.1.1.4
- UniProt
- P82896
- Pockets
- 1 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acidic phospholipase A2 5 (EC 3.1.1.4) | protein | 121 | 48% helix, 9% strand | P82896 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
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 | 978 | 0.82 | 0.83 | 84 | empty |
Interfaces
1 interface between chains.
- A–B · 838 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 4RFP · Crystal structure of a acidic PLA2 from Trimeresurus stejnegeri venom · the same entry in another collection · chain A against A, TM-score 1.00
- P82896 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 5 (P82896) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P82896
- Elsewhere: RCSB PDB 4RFP · PDBe 4RFP · UniProt P82896
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.