Research workbench
Crystal structure of lysosomal phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (hexagonal form)
Analyse Crystal structure of lysosomal phospholipase A2 crystallized in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X94
- Type
- protein
- Length
- 376 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group xv phospholipase A2
- EC
- 2.3.1.-
- UniProt
- Q8NCC3
- Ligands
- NAG, SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group xv phospholipase A2 (EC 2.3.1.-) | protein | 376 | 35% helix, 20% strand | Q8NCC3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.76 | 0.86 | 44 | empty |
| 2 | 54 | 0.39 | 0.80 | 16 | EPE |
| 3 | 63 | 0.29 | 0.74 | 17 | empty |
| 4 | 57 | 0.26 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 4X94 · Crystal structure of Lysosomal Phospholipase A2 crystallized in the presence of methyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NCC3 · AlphaFold monomer V2.0 prediction for phospholipase A2 group xv (Q8NCC3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8NCC3
- Elsewhere: RCSB PDB 4X94 · PDBe 4X94 · UniProt Q8NCC3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.