MolNFT v1 · #152741 · protein

Human LAT1-4F2HC complex bound with bch

6IRT · 4F2 cell-surface antigen heavy chain: “Human LAT1-4F2HC complex bound with bch”. Electron microscopy, 3 ligands (3PH, AUU, NAG), 14 pockets (best druggability 0.76). MolNFT v1 #152741 on GenesisL1: 3D structure, binding sites and…

PDB: 6IRT
Type: protein
Length: 926 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: 3PH, AUU, NAG
Pockets: 14 · best druggability 0.76

Structure

electron microscopy · 2 distinct chains · 49% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4F2 cell-surface antigen heavy chain	protein	469	32% helix, 16% strand	J3KPF3
B	Large neutral amino acids transporter small subunit 1	protein	457	67% helix, 0% strand	Q01650

Ligands and binding sites

3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 2 copies · chains A, B
AUU · (1S,2S,4R)-2-aminobicyclo[2.2.1]heptane-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

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	355	0.76	0.86	47	AUU
2	118	0.68	0.91	35	empty
3	649	0.65	0.75	60	empty
4	328	0.62	0.78	26	3PH
5	316	0.60	0.78	38	empty

Interfaces

1 interface between chains.

A–B · 1468 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

6IRT · human LAT1-4F2hc complex bound with BCH · 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 0.96

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 6IRT · PDBe 6IRT · UniProt J3KPF3 · UniProt Q01650

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