Research workbench
Crystal structure of lysosomal phospholipase A2 in complex with methyl arachidonyl fluorophosphonate (mafp)
Analyse Crystal structure of lysosomal phospholipase A2 in complex with methyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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