Research workbench
Crystal structure of lysosomal phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (tetragonal 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
- 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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