Research workbench
Crystal structure of human secreted phospholipase A2 group iie with compound 24
Analyse Crystal structure of human secreted phospholipase A2 group iie with compound 24 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WZU
- Type
- protein
- Length
- 123 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group iie secretory phospholipase A2
- EC
- 3.1.1.4
- UniProt
- Q9NZK7
- Ligands
- 7W3, CA, CL
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group iie secretory phospholipase A2 (EC 3.1.1.4) | protein | 123 | 49% helix, 7% strand | Q9NZK7 |
Ligands and binding sites
- 7W3 · 2-[2-methyl-3-oxamoyl-1-[[2-(trifluoromethyl) phenyl]methyl]indol-4-yl]oxyethanoic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- GOL · Glycerol · 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 | 169 | 0.51 | 0.78 | 23 | 7W3 |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5WZU · Crystal structure of human secreted phospholipase A2 group IIE with Compound 24 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZK7 · AlphaFold monomer V2.0 prediction for group iie secretory phospholipase A2 (Q9NZK7) · a predicted model of the same protein · chain A 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 Q9NZK7
- Elsewhere: RCSB PDB 5WZU · PDBe 5WZU · UniProt Q9NZK7
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