Research workbench
GLN48 PLA2 separated from vipoxin from the venom of vipera ammodytes meridionalis.
Analyse GLN48 PLA2 separated from vipoxin from the venom of vipera ammodytes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q5T
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 inhibitor
- UniProt
- P04084
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 inhibitor | protein | 122 | 45% helix, 8% strand | P04084 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.79 | 0.96 | 40 | empty |
| 2 | 57 | 0.56 | 0.89 | 12 | empty |
| 3 | 60 | 0.48 | 0.84 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1598 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1Q5T · Gln48 PLA2 separated from Vipoxin from the venom of Vipera ammodytes meridionalis. · the same entry in another collection · chain A against A, TM-score 1.00
- P04084 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 homolog vipoxin a chain… · 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 P04084
- Elsewhere: RCSB PDB 1Q5T · PDBe 1Q5T · UniProt P04084
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