MolNFT v1 · #11412 · protein
Vipoxin complex
1JLT · Phospholipase A2 inhibitor: “Vipoxin complex”. X-ray diffraction, 3 pockets (best druggability 0.84). MolNFT v1 #11412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JLT
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 inhibitor; Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P04084, P14420
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 inhibitor | protein | 122 | 49% helix, 8% strand | P04084 |
| B | Phospholipase A2 (EC 3.1.1.4) | protein | 122 | 48% helix, 11% strand | P14420 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.84 | 0.94 | 44 | MRD, MPD |
| 2 | 94 | 0.41 | 0.77 | 15 | empty |
| 3 | 66 | 0.32 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1482 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1JLT · Vipoxin Complex · 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 0.99
- P14420 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 vipoxin B chain (P14420) · a predicted model of the same protein · chain B against A, TM-score 0.99
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
- Every structure of UniProt P14420
- Elsewhere: RCSB PDB 1JLT · PDBe 1JLT · UniProt P04084 · UniProt P14420
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