MolNFT v1 · #119680 · protein
Discovery of a novel secreted phospholipase A2 (SPLA2) inhibitor.
5G3M · Group 10 secretory phospholipase A2: “Discovery of a novel secreted phospholipase A2 (SPLA2) inhibitor.”. X-ray diffraction, 2 ligands (9JH, CA), 2 pockets (best druggability 0.58). MolNFT v1 #119680 on GenesisL1: 3D structure…
- PDB
- 5G3M
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group 10 secretory phospholipase A2
- EC
- 3.1.1.4
- UniProt
- O15496
- Ligands
- 9JH, CA
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Group 10 secretory phospholipase A2 (EC 3.1.1.4) | protein | 123 | 46% helix, 7% strand | O15496 |
Ligands and binding sites
- 9JH · 4-benzylbenzamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 10 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 | 191 | 0.58 | 0.80 | 22 | PEG, 9JH |
| 2 | 211 | 0.56 | 0.79 | 24 | PEG, 9JH |
Interfaces
1 interface between chains.
- A–B · 308 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5G3M · Discovery of a novel secreted phospholipase A2 (sPLA2) inhibitor. · the same entry in another collection · chain A against A, TM-score 1.00
- O15496 · AlphaFold monomer V2.0 prediction for group 10 secretory phospholipase A2 (O15496) · 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 O15496
- Elsewhere: RCSB PDB 5G3M · PDBe 5G3M · UniProt O15496
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