MolNFT v1 · #114011 · protein
Crystal structure of escherichia COLI lgt in complex with phosphatidylglycerol and the inhibitor palmitic acid
5AZB · Prolipoprotein diacylglyceryl transferase: “Crystal structure of escherichia COLI lgt in complex with phosphatidylglycerol and the inhibitor palmitic acid”. X-ray diffraction, 2 ligands (PGT, PLM), 3 pockets (best druggability…
- PDB
- 5AZB
- Type
- protein
- Length
- 284 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolipoprotein diacylglyceryl transferase
- EC
- 2.4.99.-
- UniProt
- P60955
- Ligands
- PGT, PLM
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolipoprotein diacylglyceryl transferase (EC 2.4.99.-) | protein | 284 | 68% helix, 6% strand | P60955 |
Ligands and binding sites
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 9 copies · chains A
- PLM · Palmitic acid · ligand · 2 copies · chains A
- BOG · octyl beta-D-glucopyranoside · additive · chains A
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 | 961 | 0.80 | 0.81 | 56 | PLM, BOG, PGT |
| 2 | 206 | 0.52 | 0.77 | 23 | empty |
| 3 | 65 | 0.31 | 0.74 | 14 | PGT |
Compared structures
- 5AZB · Crystal structure of Escherichia coli Lgt in complex with phosphatidylglycerol and the… · the same entry in another collection · chain A against A, TM-score 1.00
- P60955 · AlphaFold monomer V2.0 prediction for phosphatidylglycerol-- prolipoprotein… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P60955
- Elsewhere: RCSB PDB 5AZB · PDBe 5AZB · UniProt P60955
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