Research workbench
Crystal structure of escherichia COLI lgt in complex with phosphatidylglycerol and the inhibitor palmitic acid
Analyse Crystal structure of escherichia COLI lgt in complex with phosphatidylglycerol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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