Research workbench
Structure of the human SODIUM/BILE acid cotransporter (ntcp) in complex with Fab and nanobody
Analyse Structure of the human SODIUM/BILE acid cotransporter (ntcp) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZYI
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SODIUM/BILE acid cotransporter; Heavy chain of Fab; Light chain of Fab; Nanobody
- UniProt
- Q14973
- Ligands
- CLR, CHO, NA
- Pockets
- 10 · best druggability 0.76
Structure
electron microscopy · 4 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SODIUM/BILE acid cotransporter | protein | 293 | 80% helix, 1% strand | Q14973 |
| H | Heavy chain of Fab | protein | 227 | 4% helix, 47% strand | — |
| L | Light chain of Fab | protein | 212 | 7% helix, 51% strand | — |
| K | Nanobody | protein | 120 | 3% helix, 52% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- CHO · Glycochenodeoxycholic acid · ligand · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.76 | 0.79 | 85 | CHO |
| 2 | 422 | 0.57 | 0.74 | 53 | empty |
| 3 | 100 | 0.56 | 0.85 | 20 | empty |
| 4 | 55 | 0.54 | 0.89 | 19 | empty |
| 5 | 88 | 0.42 | 0.78 | 12 | CLR |
Interfaces
4 interfaces between chains.
- H–L · 1928 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 882 Ų buried · 1 hydrogen bond · protein-protein
- L–K · 725 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 396 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7ZYI · Structure of the human sodium/bile acid cotransporter (NTCP) in complex with Fab and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q14973 · AlphaFold monomer V2.0 prediction for SODIUM/BILE acid cotransporter (Q14973) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 Q14973
- Elsewhere: RCSB PDB 7ZYI · PDBe 7ZYI · UniProt Q14973
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