Research workbench
Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state analogue
Analyse Crystal structure of bee-venom phospholipase A2 in a complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1POC
- Type
- protein
- Length
- 134 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P00630
- Ligands
- GEL, CA
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 (EC 3.1.1.4) | protein | 134 | 28% helix, 21% strand | P00630 |
Ligands and binding sites
- GEL · 1-O-octyl-2-heptylphosphonyl-sn-glycero-3-phosphoethanolamine · ligand · chains A
- CA · Calcium ion · metal · 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 | 249 | 0.62 | 0.81 | 21 | GEL |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1POC · Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state… · the same entry in another collection · chain A against A, TM-score 1.00
- P00630 · AlphaFold monomer V2.0 prediction for phospholipase A2 (P00630) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P00630
- Elsewhere: RCSB PDB 1POC · PDBe 1POC · UniProt P00630
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