Research workbench
Heteromeric amino acid transporter b0,+AT-rBAT complex bound with Arginine
Analyse Heteromeric amino acid transporter b0,+AT-rBAT complex bound with Arginine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LI9
- Type
- protein
- Length
- 2,162 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens
- Molecule
- Neutral and basic amino acid transport protein rBAT; b(0,+)-type amino acid transporter 1
- UniProt
- Q07837, P82251
- Ligands
- 3PH, ARG, NAG, CA
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · resolution 2.3 · 2 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Neutral and basic amino acid transport protein rBAT | protein | 623 | 31% helix, 19% strand | Q07837 |
| B, D | b(0,+)-type amino acid transporter 1 | protein | 458 | 66% helix, 1% strand | P82251 |
Ligands and binding sites
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 4 copies · chains A, B, C, D
- ARG · Arginine · ligand · 2 copies · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, C
- CA · Calcium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.78 | 0.81 | 80 | empty |
| 2 | 558 | 0.77 | 0.84 | 57 | ARG |
| 3 | 687 | 0.77 | 0.82 | 65 | ARG |
| 4 | 1054 | 0.74 | 0.77 | 89 | empty |
| 5 | 672 | 0.73 | 0.79 | 53 | 3PH |
Interfaces
4 interfaces between chains.
- C–D · 1622 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1619 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 948 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 56 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 6LI9 · Heteromeric amino acid transporter B0,+AT-rbat complex bound with arginine · the same entry in another collection · chain D against D, TM-score 1.00
- Q07837 · AlphaFold monomer V2.0 prediction for neutral and basic amino acid transport protein rbat… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P82251 · AlphaFold monomer V2.0 prediction for B(0,+)-type amino acid transporter 1 (P82251) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q07837
- Every structure of UniProt P82251
- Elsewhere: RCSB PDB 6LI9 · PDBe 6LI9 · UniProt Q07837 · UniProt P82251
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