Research workbench
Crystal structure of acidic phospholipase A2 from deinagkistrodon acutus
Analyse Crystal structure of acidic phospholipase A2 from deinagkistrodon acutus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IJL
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- Q7SID6
- Ligands
- CA, ZN
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 (EC 3.1.1.4) | protein | 123 | 47% helix, 7% strand | Q7SID6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.75 | 0.90 | 27 | empty |
| 2 | 101 | 0.61 | 0.87 | 18 | empty |
| 3 | 96 | 0.39 | 0.77 | 18 | empty |
| 4 | 78 | 0.38 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1006 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1IJL · Crystal structure of acidic phospholipase A2 from deinagkistrodon acutus · the same entry in another collection · chain A against A, TM-score 1.00
- Q7SID6 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 (Q7SID6) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q7SID6
- Elsewhere: RCSB PDB 1IJL · PDBe 1IJL · UniProt Q7SID6
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