Research workbench
Crystal structure of trkb-D5 bound to neurotrophin-4/5
Analyse Crystal structure of trkb-D5 bound to neurotrophin-4/5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HCF
- Type
- protein
- Length
- 444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurotrophin-4; BDNF/NT-3 growth factors receptor
- UniProt
- P34130, Q16620
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neurotrophin-4 | protein | 121 | 2% helix, 54% strand | P34130 |
| B | Neurotrophin-4 | protein | 121 | 0% helix, 49% strand | P34130 |
| X, Y | BDNF/NT-3 growth factors receptor | protein | 101 | 3% helix, 61% strand | Q16620 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.79 | 0.89 | 62 | empty |
| 2 | 93 | 0.77 | 0.98 | 24 | empty |
| 3 | 107 | 0.43 | 0.78 | 21 | empty |
| 4 | 94 | 0.41 | 0.78 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1749 Ų buried · 24 hydrogen bonds · protein-protein
- A–X · 810 Ų buried · 7 hydrogen bonds · protein-protein
- B–Y · 713 Ų buried · 6 hydrogen bonds · protein-protein
- B–X · 398 Ų buried · 4 hydrogen bonds · protein-protein
- A–Y · 380 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1HCF · Crystal structure of TrkB-d5 bound to neurotrophin-4/5 · the same entry in another collection · chain A against A, 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 0.98
- P34130 · AlphaFold monomer V2.0 prediction for neurotrophin-4 (P34130) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P34130
- Every structure of UniProt Q16620
- Elsewhere: RCSB PDB 1HCF · PDBe 1HCF · UniProt P34130 · UniProt Q16620
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