MolNFT v1 · #109652 · protein
Crystal structure of lysosomal phospholipase A2 in complex with methyl arachidonyl fluorophosphonate (mafp)
4X97 · Group xv phospholipase A2: “Crystal structure of lysosomal phospholipase A2 in complex with methyl arachidonyl fluorophosphonate (mafp)”. X-ray diffraction, 4 ligands (MAY, NAG, PO4), 13 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 4X97
- Type
- protein
- Length
- 1,506 residues
- Chains
- 4
- 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, PO4, CL
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Group xv phospholipase A2 (EC 2.3.1.-) | protein | 377 | 36% helix, 20% strand | Q8NCC3 |
| C, D | Group xv phospholipase A2 (EC 2.3.1.-) | protein | 376 | 36% helix, 20% strand | Q8NCC3 |
Ligands and binding sites
- MAY · Methyl arachidonyl fluorophosphonate · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, D, B, C
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.79 | 0.82 | 79 | empty |
| 2 | 404 | 0.79 | 0.87 | 42 | MAY |
| 3 | 595 | 0.77 | 0.83 | 56 | MAY |
| 4 | 623 | 0.77 | 0.82 | 55 | MAY |
| 5 | 568 | 0.76 | 0.82 | 49 | MAY |
Interfaces
5 interfaces between chains.
- A–D · 427 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 384 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 327 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 229 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 glycan, 5 disulfide, 4 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
- 4X97 · Crystal structure of Lysosomal Phospholipase A2 in complex with methyl arachidonyl… · 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 1.00
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 4X97 · PDBe 4X97 · UniProt Q8NCC3
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