MolNFT v1 · #137533 · protein
Apolipoprotein N-acyltransferase C387S active site mutant
5VRH: “Apolipoprotein N-acyltransferase C387S active site mutant”. X-ray diffraction, 4 ligands (OLB, PLM, MG), 4 pockets (best druggability 0.77). MolNFT v1 #137533 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VRH
- Type
- protein
- Length
- 490 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
- OLB, PLM, MG, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apolipoprotein N-acyltransferase (EC 2.3.1.-) | protein | 490 | 52% helix, 16% strand | P23930 |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A
- PLM · Palmitic acid · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 2 copies · 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 | 571 | 0.77 | 0.83 | 46 | CL, OLC |
| 2 | 197 | 0.59 | 0.81 | 28 | empty |
| 3 | 74 | 0.37 | 0.76 | 11 | empty |
| 4 | 82 | 0.33 | 0.73 | 16 | empty |
Compared structures
- 5VRH · Apolipoprotein N-acyltransferase C387S active site mutant · 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 1.00
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 5VRH · PDBe 5VRH · UniProt P23930
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