Research workbench
Cryo-EM structure of human ntcp complexed with YN69202FAB in the presence of myristoylated PRES1 peptide
Analyse Cryo-EM structure of human ntcp complexed with YN69202FAB in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VAG
- Type
- protein
- Length
- 743 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SODIUM/BILE acid cotransporter; Fab heavy chain from antibody IgG clone number YN69202…
- UniProt
- Q14973
- Pockets
- 10 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SODIUM/BILE acid cotransporter | protein | 306 | 76% helix, 0% strand | Q14973 |
| H | Fab heavy chain from antibody IgG clone number YN69202 | protein | 221 | 4% helix, 46% strand | — |
| L | Fab light chain from antibody IgG clone number YN69202 | protein | 216 | 4% helix, 38% strand | — |
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 | 1158 | 0.76 | 0.78 | 82 | empty |
| 2 | 186 | 0.60 | 0.82 | 27 | empty |
| 3 | 418 | 0.58 | 0.75 | 54 | empty |
| 4 | 184 | 0.55 | 0.79 | 30 | empty |
| 5 | 55 | 0.50 | 0.86 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1778 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 747 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 416 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7VAG · Cryo-EM structure of human NTCP complexed with YN69202Fab in the presence of… · 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 0.78
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 7VAG · PDBe 7VAG · UniProt Q14973
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