MolNFT v1 · #9157 · protein
Prophospholipase A2 dimer complexed with MJ33, sulfate, and calcium
1HN4: “Prophospholipase A2 dimer complexed with MJ33, sulfate, and calcium”. X-ray diffraction, 3 ligands (MJI, CA, SO4), 1 pocket (best druggability 0.83). MolNFT v1 #9157 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1HN4
- Type
- protein
- Length
- 256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prophospholipase A2
- EC
- 3.1.1.4
- UniProt
- P00592
- Ligands
- MJI, CA, SO4
- Pockets
- 1 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prophospholipase A2 (EC 3.1.1.4) | protein | 129 | 56% helix, 9% strand | P00592 |
| B | Prophospholipase A2 (EC 3.1.1.4) | protein | 127 | 53% helix, 9% strand | P00592 |
Ligands and binding sites
- MJI · 1-hexadecyl-3-trifluoroethyl-sn-glycero-2-phosphate methane · ligand · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
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 | 844 | 0.83 | 0.85 | 86 | MJI, SO4 |
Interfaces
1 interface between chains.
- A–B · 769 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1HN4 · Prophospholipase A2 dimer complexed with MJ33, sulfate, and calcium · 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 0.92
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 1HN4 · PDBe 1HN4 · UniProt P00592
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