MolNFT v1 · #176616 · protein
Overall structure of the LAT1-4F2HC bound with jx-075
7DSK · 4F2 cell-surface antigen heavy chain: “Overall structure of the LAT1-4F2HC bound with jx-075”. Electron microscopy, 4 ligands (Y01, 3PH, HNX), 10 pockets (best druggability 0.84). MolNFT v1 #176616 on GenesisL1: 3D structure…
- PDB
- 7DSK
- Type
- protein
- Length
- 935 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4F2 cell-surface antigen heavy chain; Large neutral amino acids transporter small subunit…
- UniProt
- J3KPF3, Q01650
- Ligands
- Y01, 3PH, HNX, NAG
- Pockets
- 10 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4F2 cell-surface antigen heavy chain | protein | 471 | 32% helix, 14% strand | J3KPF3 |
| B | Large neutral amino acids transporter small subunit 1 | protein | 464 | 68% helix, 2% strand | Q01650 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 2 copies · chains A, B
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · chains A, B
- HNX · (2~{S})-2-azanyl-7-(naphthalen-1-ylmethoxy)-3,4-dihydro-1~{H}-naphthalene-2-carboxylic acid · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.84 | 0.93 | 41 | HNX |
| 2 | 677 | 0.63 | 0.73 | 65 | empty |
| 3 | 258 | 0.61 | 0.80 | 38 | empty |
| 4 | 377 | 0.59 | 0.75 | 21 | Y01 |
| 5 | 294 | 0.54 | 0.75 | 37 | 3PH |
Interfaces
1 interface between chains.
- A–B · 1528 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 7DSK · Overall structure of the LAT1-4F2hc bound with JX-075 · the same entry in another collection · chain A against A, TM-score 1.00
- Q01650 · AlphaFold monomer V2.0 prediction for large neutral amino acids transporter small subunit… · a predicted model of the same protein · chain B against A, TM-score 0.90
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 J3KPF3
- Every structure of UniProt Q01650
- Elsewhere: RCSB PDB 7DSK · PDBe 7DSK · UniProt J3KPF3 · UniProt Q01650
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.