Research workbench
Crystal structure of human secreted phospholipase A2 group iie with compound 8
Analyse Crystal structure of human secreted phospholipase A2 group iie with compound 8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WZS
- 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
- 7W9, CA, CL
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group iie secretory phospholipase A2 (EC 3.1.1.4) | protein | 123 | 50% helix, 7% strand | Q9NZK7 |
Ligands and binding sites
- 7W9 · 2-[2-methyl-1-(naphthalen-1-ylmethyl)-3-oxamoyl-indol-4-yl]oxyethanoic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · 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
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 | 200 | 0.57 | 0.80 | 25 | 7W9 |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5WZS · Crystal structure of human secreted phospholipase A2 group IIE with Compound 8 · 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 0.96
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 5WZS · PDBe 5WZS · UniProt Q9NZK7
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