MolNFT v1 · #109646 · protein
Crystal structure of lysosomal phospholipase A2 in complex with isopropyl dodec-11-enylfluorophosphonate (idfp)
4X91 · Group xv phospholipase A2: “Crystal structure of lysosomal phospholipase A2 in complex with isopropyl dodec-11-enylfluorophosphonate…”. X-ray diffraction, 3 ligands (TO4, NAG, PO4), 10 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 4X91
- Type
- protein
- Length
- 1,504 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
- TO4, NAG, PO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Group xv phospholipase A2 (EC 2.3.1.-) | protein | 376 | 35% helix, 20% strand | Q8NCC3 |
Ligands and binding sites
- TO4 · propan-2-yl (R)-dodec-11-en-1-ylphosphonofluoridate · 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 · 10 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, D, B, C
- 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.81 | 0.86 | 45 | TO4, MPD |
| 2 | 552 | 0.80 | 0.86 | 47 | TO4, MPD |
| 3 | 589 | 0.77 | 0.83 | 52 | TO4, MPD |
| 4 | 557 | 0.77 | 0.83 | 50 | TO4, MPD |
| 5 | 1069 | 0.77 | 0.79 | 86 | MPD |
Interfaces
5 interfaces between chains.
- A–B · 351 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 344 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 312 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 306 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 304 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 8 disulfide, 4 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
- 4X91 · Crystal structure of Lysosomal Phospholipase A2 in complex with Isopropyl… · the same entry in another collection · chain C against C, 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 4X91 · PDBe 4X91 · UniProt Q8NCC3
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