MolNFT v1 · #109648 · protein
Crystal structure of lysosomal phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (tetragonal form)
4X93 · Group xv phospholipase A2: “Crystal structure of lysosomal phospholipase A2 crystallized in the presence of methyl arachidonyl…”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.80). MolNFT v1 #109648 on GenesisL1…
- PDB
- 4X93
- Type
- protein
- Length
- 753 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
- NAG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 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 |
| B | Group xv phospholipase A2 (EC 2.3.1.-) | protein | 377 | 35% helix, 20% strand | Q8NCC3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.80 | 0.89 | 51 | PEG |
| 2 | 330 | 0.80 | 0.90 | 40 | empty |
| 3 | 636 | 0.71 | 0.79 | 58 | empty |
| 4 | 57 | 0.38 | 0.79 | 12 | EPE |
| 5 | 58 | 0.37 | 0.79 | 12 | EPE |
Interfaces
1 interface between chains.
- A–B · 433 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 4X93 · 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 B 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 4X93 · PDBe 4X93 · UniProt Q8NCC3
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