MolNFT v1 · #119681 · protein
Discovery of a novel secreted phospholipase A2 (SPLA2) inhibitor.
5G3N · Phospholipase A2, membrane associated: “Discovery of a novel secreted phospholipase A2 (SPLA2) inhibitor.”. X-ray diffraction, 2 ligands (X28, CA), 2 pockets (best druggability 0.56). MolNFT v1 #119681 on GenesisL1: 3D structure…
- PDB
- 5G3N
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2, membrane associated
- EC
- 3.1.1.4
- UniProt
- P14555
- Ligands
- X28, CA
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2, membrane associated (EC 3.1.1.4) | protein | 127 | 50% helix, 6% strand | P14555 |
| B | Phospholipase A2, membrane associated (EC 3.1.1.4) | protein | 124 | 50% helix, 6% strand | P14555 |
Ligands and binding sites
- X28 · 3-(5'-benzyl-2'-carbamoylbiphenyl-3-yl)propanoic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.56 | 0.80 | 22 | X28 |
| 2 | 169 | 0.56 | 0.81 | 23 | X28 |
Interfaces
1 interface between chains.
- A–B · 437 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5G3N · Discovery of a novel secreted phospholipase A2 (sPLA2) inhibitor. · the same entry in another collection · chain A against A, TM-score 1.00
- P14555 · AlphaFold monomer V2.0 prediction for phospholipase A2, membrane associated (P14555) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P14555
- Elsewhere: RCSB PDB 5G3N · PDBe 5G3N · UniProt P14555
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