Research workbench
Phospholipase A2 from vipera ammodytes meridionalis
Analyse Phospholipase A2 from vipera ammodytes meridionalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RGB
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P14420
- Ligands
- ELD
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K, L | Phospholipase A2 (EC 3.1.1.4) | protein | 122 | 39% helix, 7% strand | P14420 |
Ligands and binding sites
- ELD · (9E)-octadec-9-enamide · ligand · 2 copies · chains A, B, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.84 | 0.92 | 46 | ELD |
| 2 | 456 | 0.82 | 0.89 | 64 | ELD |
| 3 | 110 | 0.52 | 0.82 | 19 | empty |
| 4 | 102 | 0.47 | 0.80 | 15 | empty |
| 5 | 101 | 0.47 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1392 Ų buried · 11 hydrogen bonds · protein-protein
- K–L · 1361 Ų buried · 10 hydrogen bonds · protein-protein
- B–L · 89 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 1RGB · Phospholipase A2 from Vipera ammodytes meridionalis · the same entry in another collection · chain A against A, TM-score 1.00
- P14420 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 vipoxin B chain (P14420) · 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 P14420
- Elsewhere: RCSB PDB 1RGB · PDBe 1RGB · UniProt P14420
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