MolNFT v1 · #18976 · protein
GLN48 PLA2 separated from vipoxin from the venom of vipera ammodytes meridionalis.
1Q5T · Phospholipase A2 inhibitor: “GLN48 PLA2 separated from vipoxin from the venom of vipera ammodytes meridionalis.”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.79). MolNFT v1 #18976 on GenesisL1: 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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