Research workbench
Structural insights into lipoprotein N-acylation by escherichia COLI apolipoprotein N-acyltransferase
Analyse Structural insights into lipoprotein N-acylation by escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VRG
- Type
- protein
- Length
- 494 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apolipoprotein N-acyltransferase
- EC
- 2.3.1.-
- UniProt
- P23930
- Ligands
- PLM, LNK, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apolipoprotein N-acyltransferase (EC 2.3.1.-) | protein | 494 | 51% helix, 18% strand | P23930 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 5 copies · chains A
- LNK · Pentane · ligand · chains A
- CL · Chloride ion · ion · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.76 | 0.83 | 49 | OLC, PLM, CL |
| 2 | 172 | 0.56 | 0.81 | 24 | empty |
| 3 | 79 | 0.32 | 0.73 | 16 | PLM |
| 4 | 56 | 0.30 | 0.74 | 13 | empty |
Compared structures
- 5VRG · Structural insights into lipoprotein N-acylation by Escherichia coli apolipoprotein… · the same entry in another collection · chain A against A, TM-score 1.00
- P23930 · AlphaFold monomer V2.0 prediction for apolipoprotein N-acyltransferase (P23930) · a predicted model of the same protein · chain A 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 P23930
- Elsewhere: RCSB PDB 5VRG · PDBe 5VRG · UniProt P23930
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