MolNFT v1 · #127159 · protein
Structure of human trkb receptor ligand binding domain in complex with the Fab frgment of antibody AB20
5MO9 · AB20 Fab heavy chain: “Structure of human trkb receptor ligand binding domain in complex with the Fab frgment of antibody AB20”. X-ray diffraction, 5 pockets (best druggability 0.52). MolNFT v1 #127159 on GenesisL1: 3D structure…
- PDB
- 5MO9
- Type
- protein
- Length
- 533 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AB20 Fab heavy chain; AB20 Fab light chain; BDNF/NT-3 growth factors receptor
- EC
- 2.7.10.1
- UniProt
- Q16620
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | AB20 Fab heavy chain | protein | 212 | 6% helix, 54% strand | — |
| L | AB20 Fab light chain | protein | 219 | 5% helix, 51% strand | — |
| X | BDNF/NT-3 growth factors receptor (EC 2.7.10.1) | protein | 102 | 3% helix, 59% strand | Q16620 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.52 | 0.75 | 43 | empty |
| 2 | 356 | 0.51 | 0.72 | 47 | empty |
| 3 | 129 | 0.40 | 0.74 | 27 | empty |
| 4 | 69 | 0.31 | 0.74 | 15 | empty |
| 5 | 67 | 0.30 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1716 Ų buried · 10 hydrogen bonds · protein-protein
- H–X · 487 Ų buried · 5 hydrogen bonds · protein-protein
- L–X · 414 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5MO9 · Structure of human TrkB receptor ligand binding domain in complex with the Fab frgment of… · the same entry in another collection · chain H against H, TM-score 1.00
- Q16620 · AlphaFold monomer V2.0 prediction for BDNF/NT-3 growth factors receptor (Q16620) · a predicted model of the same protein · chain X against A, TM-score 0.91
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 Q16620
- Elsewhere: RCSB PDB 5MO9 · PDBe 5MO9 · UniProt Q16620
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