Research workbench
Structure of vcindy-na-FAB84 in nanodisc
Analyse Structure of vcindy-na-FAB84 in nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WW5
- Type
- protein
- Length
- 1,764 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dass family sodium-coupled anion symporter; FAB84 heavy chain; FAB84 light chain
- UniProt
- A0A0H3AG83
- Ligands
- 6PE
- Pockets
- 18 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dass family sodium-coupled anion symporter | protein | 445 | 73% helix, 0% strand | A0A0H3AG83 |
| C, E | FAB84 heavy chain | protein | 228 | 3% helix, 43% strand | — |
| F, D | FAB84 light chain | protein | 209 | 6% helix, 44% strand | — |
Ligands and binding sites
- 6PE · 1,2-dihexanoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, B
- HEX · Hexane · additive · 2 copies · chains A, B
- OCT · N-octane · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.79 | 0.99 | 16 | empty |
| 2 | 918 | 0.77 | 0.80 | 123 | empty |
| 3 | 405 | 0.67 | 0.80 | 51 | empty |
| 4 | 421 | 0.66 | 0.79 | 52 | empty |
| 5 | 345 | 0.54 | 0.74 | 52 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2167 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1829 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1810 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 748 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 732 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6WW5 · Structure of VcINDY-Na-Fab84 in nanodisc · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0H3AG83
- Elsewhere: RCSB PDB 6WW5 · PDBe 6WW5 · UniProt A0A0H3AG83
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