Research workbench
Overall structure of the LAT1-4F2HC bound with jx-119
Analyse Overall structure of the LAT1-4F2HC bound with jx-119 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DSN
- 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, HO9, NAG
- Pockets
- 10 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4F2 cell-surface antigen heavy chain | protein | 471 | 30% helix, 16% strand | J3KPF3 |
| B | Large neutral amino acids transporter small subunit 1 | protein | 464 | 66% 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
- HO9 · (2~{S})-2-azanyl-7-[[2-(1,3-benzoxazol-2-yl) phenyl]methoxy]-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 | 559 | 0.82 | 0.87 | 56 | HO9 |
| 2 | 249 | 0.61 | 0.80 | 40 | empty |
| 3 | 362 | 0.59 | 0.76 | 23 | Y01 |
| 4 | 276 | 0.53 | 0.74 | 31 | 3PH |
| 5 | 249 | 0.52 | 0.75 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1510 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 7DSN · Overall structure of the LAT1-4F2hc bound with JX-119 · 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 7DSN · PDBe 7DSN · UniProt J3KPF3 · UniProt Q01650
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