MolNFT v1 · #21609 · protein
Crystal structure of the receptor-ligand complex between nerve growth factor and the common neurotrophin receptor P75
1SG1 · Beta-nerve growth factor: “Crystal structure of the receptor-ligand complex between nerve growth factor and the common neurotrophin…”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.79). MolNFT v1 #21609 on…
- PDB
- 1SG1
- Type
- protein
- Length
- 361 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-nerve growth factor; Tumor necrosis factor receptor superfamily member 16
- UniProt
- P01138, P07174
- Ligands
- CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-nerve growth factor | protein | 99 | 0% helix, 63% strand | P01138 |
| B | Beta-nerve growth factor | protein | 102 | 0% helix, 59% strand | P01138 |
| X | Tumor necrosis factor receptor superfamily member 16 | protein | 160 | 0% helix, 34% strand | P07174 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 240 | 0.79 | 0.91 | 34 | empty |
| 2 | 725 | 0.72 | 0.78 | 59 | CL |
| 3 | 155 | 0.44 | 0.75 | 30 | empty |
| 4 | 90 | 0.34 | 0.74 | 20 | empty |
| 5 | 51 | 0.31 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1467 Ų buried · 15 hydrogen bonds · protein-protein
- A–X · 655 Ų buried · 5 hydrogen bonds · protein-protein
- B–X · 644 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 1SG1 · Crystal Structure of the Receptor-Ligand Complex between Nerve Growth Factor and the… · the same entry in another collection · chain A against A, TM-score 1.00
- P07174 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain X against A, TM-score 0.91
- P01138 · AlphaFold monomer V2.0 prediction for beta-nerve growth factor (P01138) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P01138
- Every structure of UniProt P07174
- Elsewhere: RCSB PDB 1SG1 · PDBe 1SG1 · UniProt P01138 · UniProt P07174
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