MolNFT v1 · #149611 · protein
Secreted phospholipase A2 type X in complex with ligand
6G5J · Group 10 secretory phospholipase A2: “Secreted phospholipase A2 type X in complex with ligand”. X-ray diffraction, 2 ligands (EM8, CA), 3 pockets (best druggability 0.55). MolNFT v1 #149611 on GenesisL1: 3D structure, binding sites…
- PDB
- 6G5J
- Type
- protein
- Length
- 245 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
- EM8, CA
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group 10 secretory phospholipase A2 (EC 3.1.1.4) | protein | 122 | 47% helix, 9% strand | O15496 |
| B | Group 10 secretory phospholipase A2 (EC 3.1.1.4) | protein | 123 | 46% helix, 9% strand | O15496 |
Ligands and binding sites
- EM8 · (3~{R})-3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy) indol-1-yl]phenyl]butanoic acid · ligand · 3 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.55 | 0.79 | 26 | EM8 |
| 2 | 200 | 0.54 | 0.78 | 23 | EM8 |
| 3 | 53 | 0.31 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 313 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6G5J · Secreted phospholipase A2 type X in complex with ligand · 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 6G5J · PDBe 6G5J · UniProt O15496
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