MolNFT v2 · #214793 · protein
SLC15A4 inhibitor complex
8JZX · lysosomal transporter,ALFA tag,lysosomal transporter: “SLC15A4 inhibitor complex”. Electron microscopy at 2.5, 3 ligands (CLR, Q09, NAG), 10 pockets (best druggability 0.81). MolNFT v2 #214793 on GenesisL1: 3D structure, binding…
- PDB
- 8JZX
- Type
- protein
- Length
- 910 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Homo sapiens; synthetic construct
- Molecule
- lysosomal transporter,ALFA tag,lysosomal transporter
- UniProt
- Q8N697
- Ligands
- CLR, Q09, NAG
- Pockets
- 10 · best druggability 0.81
Structure
electron microscopy · resolution 2.5 · 1 distinct chain · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | lysosomal transporter,ALFA tag,lysosomal transporter | protein | 455 | 73% helix, 3% strand | Q8N697 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 4 copies · chains A, B
- Q09 · 2-(4-ethoxyphenyl)-N-[3-[(2R)-2-methylpiperidin-1-yl]propyl]quinoline-4-carboxamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.81 | 0.82 | 73 | Q09 |
| 2 | 1080 | 0.80 | 0.81 | 71 | Q09 |
| 3 | 716 | 0.74 | 0.78 | 44 | CLR |
| 4 | 663 | 0.68 | 0.76 | 63 | CLR |
| 5 | 86 | 0.36 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 719 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- Q8N697 · AlphaFold monomer V2.0 prediction for solute carrier family 15 member 4 (Q8N697) · a predicted model of the same protein · chain A against A, TM-score 0.74
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 Q8N697
- Elsewhere: RCSB PDB 8JZX · PDBe 8JZX · UniProt Q8N697
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