MolNFT v1 · #176622 · protein
Overall structure of the LAT1-4F2HC bound with 3,5-diiodo-L-tyrosine
7DSQ · 4F2 cell-surface antigen heavy chain: “Overall structure of the LAT1-4F2HC bound with 3,5-diiodo-L-tyrosine”. Electron microscopy, 4 ligands (Y01, TYI, 3PH), 13 pockets (best druggability 0.81). MolNFT v1 #176622 on GenesisL1: 3D…
- PDB
- 7DSQ
- Type
- protein
- Length
- 934 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, TYI, 3PH, NAG
- Pockets
- 13 · best druggability 0.81
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 | 470 | 33% helix, 16% strand | J3KPF3 |
| B | Large neutral amino acids transporter small subunit 1 | protein | 464 | 67% helix, 1% strand | Q01650 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 2 copies · chains A, B
- TYI · 3,5-diiodotyrosine · ligand · chains B
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · chains A, 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
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.81 | 0.90 | 53 | TYI |
| 2 | 388 | 0.60 | 0.76 | 22 | Y01 |
| 3 | 199 | 0.57 | 0.80 | 31 | empty |
| 4 | 303 | 0.55 | 0.75 | 39 | empty |
| 5 | 238 | 0.48 | 0.73 | 30 | 3PH |
Interfaces
1 interface between chains.
- A–B · 1464 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 7DSQ · Overall structure of the LAT1-4F2hc bound with 3,5-diiodo-L-tyrosine · 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 0.89
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 7DSQ · PDBe 7DSQ · UniProt J3KPF3 · UniProt Q01650
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