Research workbench
Carboxylic ester hydrolase complex (dimeric PLA2 + lpc-ether + acetate + phosphate ions)
Analyse Carboxylic ester hydrolase complex (dimeric PLA2 + lpc-ether + acetate +… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L8S
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2, major isoenzyme
- EC
- 3.1.1.4
- UniProt
- P00592
- Ligands
- LPE, CA, NA, PO4
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2, major isoenzyme (EC 3.1.1.4) | protein | 124 | 52% helix, 9% strand | P00592 |
Ligands and binding sites
- LPE · 1-O-octadecyl-sn-glycero-3-phosphocholine · ligand · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.78 | 0.83 | 69 | ACT, LPE |
Interfaces
1 interface between chains.
- A–B · 812 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1L8S · CARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + LPC-ether + ACETATE + PHOSPHATE IONS) · the same entry in another collection · chain A against A, TM-score 1.00
- P00592 · AlphaFold monomer V2.0 prediction for phospholipase A2, major isoenzyme (P00592) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P00592
- Elsewhere: RCSB PDB 1L8S · PDBe 1L8S · UniProt P00592
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