MolNFT v1 · #123839 · protein
Structure of lipid phosphate phosphatase pgpb complex with pe
5JWY · Phosphatidylglycerophosphatase B: “Structure of lipid phosphate phosphatase pgpb complex with pe”. X-ray diffraction, 1 ligand (46E), 1 pocket (best druggability 0.70). MolNFT v1 #123839 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5JWY
- Type
- protein
- Length
- 259 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylglycerophosphatase B
- EC
- 3.1.3.27, 3.1.3.81, 3.1.3.4, 3.6.1.27
- UniProt
- P0A924
- Ligands
- 46E
- Pockets
- 1 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylglycerophosphatase B (EC 3.1.3.27, 3.1.3.81, 3.1.3.4, 3.6.1.27) | protein | 259 | 78% helix, 0% strand | P0A924 |
Ligands and binding sites
- 46E · (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.70 | 0.79 | 40 | 46E |
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 5JWY · Structure of lipid phosphate phosphatase PgpB complex with PE · the same entry in another collection · chain A against A, TM-score 1.00
- P0A924 · AlphaFold monomer V2.0 prediction for phosphatidylglycerophosphatase B (P0A924) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P0A924
- Elsewhere: RCSB PDB 5JWY · PDBe 5JWY · UniProt P0A924
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