MolNFT v1 · #18414 · protein
Crystal structure of cobra-venom phospholipase A2 in a complex with a transition-state analogue
1POB: “Crystal structure of cobra-venom phospholipase A2 in a complex with a transition-state analogue”. X-ray diffraction, 2 ligands (GEL, CA), 2 pockets (best druggability 0.61). MolNFT v1 #18414 on GenesisL1: 3D structure, binding sites…
- PDB
- 1POB
- Type
- protein
- Length
- 236 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P00598
- Ligands
- GEL, CA
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 (EC 3.1.1.4) | protein | 118 | 47% helix, 9% strand | P00598 |
Ligands and binding sites
- GEL · 1-O-octyl-2-heptylphosphonyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 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 | 196 | 0.61 | 0.82 | 23 | GEL |
| 2 | 189 | 0.56 | 0.79 | 21 | GEL |
Interfaces
1 interface between chains.
- A–B · 311 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1POB · Crystal structure of cobra-venom phospholipase A2 in a complex with a transition-state… · the same entry in another collection · chain A against A, TM-score 1.00
- P00598 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 1 (P00598) · 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 P00598
- Elsewhere: RCSB PDB 1POB · PDBe 1POB · UniProt P00598
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