Research workbench
Zebrafish SLC38A9 with arginine bound in the cytosol open state
Analyse Zebrafish SLC38A9 with arginine bound in the cytosol open state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C08
- Type
- protein
- Length
- 1,607 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab heavy chain; Antibody Fab light chain; Sodium-coupled neutral amino acid…
- UniProt
- Q08BA4
- Ligands
- ARG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Antibody Fab heavy chain | protein | 214 | 6% helix, 50% strand | — |
| B, E | Antibody Fab light chain | protein | 215 | 6% helix, 52% strand | — |
| C | Sodium-coupled neutral amino acid transporter 9 | protein | 364 | 68% helix, 0% strand | Q08BA4 |
| F | Sodium-coupled neutral amino acid transporter 9 | protein | 385 | 63% helix, 0% strand | Q08BA4 |
Ligands and binding sites
- ARG · Arginine · ligand · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.77 | 0.83 | 71 | empty |
| 2 | 757 | 0.76 | 0.81 | 66 | ARG |
| 3 | 488 | 0.69 | 0.80 | 55 | empty |
| 4 | 60 | 0.68 | 0.95 | 20 | empty |
| 5 | 218 | 0.68 | 0.85 | 35 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1778 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1767 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 608 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 586 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 479 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6C08 · Zebrafish SLC38A9 with arginine bound in the cytosol open state · the same entry in another collection · chain F against F, TM-score 1.00
- Q08BA4 · AlphaFold monomer V2.0 prediction for sodium-coupled neutral amino acid transporter 9… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q08BA4
- Elsewhere: RCSB PDB 6C08 · PDBe 6C08 · UniProt Q08BA4
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