MolNFT v1 · #104867 · protein
Crystal structure of phospholipase a 1 from HORNET(VESPA basalis) venom
4QNN: “Crystal structure of phospholipase a 1 from HORNET(VESPA basalis) venom”. X-ray diffraction, 2 ligands (HG, CL), 6 pockets (best druggability 0.79). MolNFT v1 #104867 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QNN
- Type
- protein
- Length
- 1,188 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase a 1 from HORNET(VESPA basalis) venom
- Ligands
- HG, CL
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phospholipase a 1 from HORNET(VESPA basalis) venom | protein | 297 | 31% helix, 19% strand | — |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 24 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.79 | 0.80 | 85 | CL |
| 2 | 1180 | 0.79 | 0.80 | 93 | empty |
| 3 | 685 | 0.67 | 0.76 | 57 | CL |
| 4 | 289 | 0.55 | 0.76 | 40 | CL, HG |
| 5 | 79 | 0.37 | 0.77 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 741 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 700 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 397 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 337 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4QNN · Crystal Structure of phospholipase A 1 from hornet(Vespa basalis) venom · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4QNN · PDBe 4QNN
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