MolNFT v1 · #171138 · protein
Heterotetrameric structure of the rbat-B(0,+)AT1 complex
6YUP · Neutral and basic amino acid transport protein rbat: “Heterotetrameric structure of the rbat-B(0,+)AT1 complex”. Electron microscopy, 2 ligands (NAG, CA), 20 pockets (best druggability 0.80). MolNFT v1 #171138 on GenesisL1: 3D…
- PDB
- 6YUP
- Type
- protein
- Length
- 1,844 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutral and basic amino acid transport protein rbat; B(0,+)-type amino acid transporter 1
- UniProt
- Q07837, P82251
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 41% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Neutral and basic amino acid transport protein rbat | protein | 594 | 27% helix, 16% strand | Q07837 |
| D, E | B(0,+)-type amino acid transporter 1 | protein | 328 | 67% helix, 1% strand | P82251 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.80 | 0.81 | 148 | empty |
| 2 | 827 | 0.72 | 0.77 | 76 | empty |
| 3 | 725 | 0.71 | 0.77 | 64 | empty |
| 4 | 531 | 0.70 | 0.80 | 53 | empty |
| 5 | 463 | 0.67 | 0.79 | 56 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1033 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 905 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 897 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 6YUP · Heterotetrameric structure of the rBAT-b(0,+)AT1 complex · the same entry in another collection · chain A against A, 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 0.98
- P82251 · AlphaFold monomer V2.0 prediction for B(0,+)-type amino acid transporter 1 (P82251) · a predicted model of the same protein · chain D 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 Q07837
- Every structure of UniProt P82251
- Elsewhere: RCSB PDB 6YUP · PDBe 6YUP · UniProt Q07837 · UniProt P82251
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