MolNFT v1 · #109650 · protein
Crystal structure of fully glycosylated lysosomal phospholipase A2 in complex with methyl arachidonyl fluorophosphonate (mafp)
4X95 · Group xv phospholipase A2: “Crystal structure of fully glycosylated lysosomal phospholipase A2 in complex with methyl arachidonyl…”. X-ray diffraction, 3 ligands (MAY, NAG, BMA), 3 pockets (best druggability 0.81). MolNFT v1 #109650…
- PDB
- 4X95
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group xv phospholipase A2
- EC
- 2.3.1.-
- UniProt
- Q8NCC3
- Ligands
- MAY, NAG, BMA
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group xv phospholipase A2 (EC 2.3.1.-) | protein | 375 | 37% helix, 21% strand | Q8NCC3 |
| B | Group xv phospholipase A2 (EC 2.3.1.-) | protein | 377 | 37% helix, 21% strand | Q8NCC3 |
Ligands and binding sites
- MAY · Methyl arachidonyl fluorophosphonate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.81 | 0.89 | 60 | empty |
| 2 | 513 | 0.78 | 0.84 | 52 | MAY |
| 3 | 418 | 0.77 | 0.86 | 51 | MAY |
Interfaces
1 interface between chains.
- A–B · 1203 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 covalent, 2 disulfide (N-glycosylation, covalent ligand, disulfide).
Compared structures
- 4X95 · Crystal structure of fully glycosylated Lysosomal Phospholipase A2 in complex with 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 4X95 · PDBe 4X95 · UniProt Q8NCC3
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