MolNFT v1 · #40092 · protein
Structure of the extracellular segment of human trka in complex with nerve growth factor
2IFG · High affinity nerve growth factor receptor: “Structure of the extracellular segment of human trka in complex with nerve growth factor”. X-ray diffraction, 4 ligands (NAG, NDG, BMA), 14 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 2IFG
- Type
- protein
- Length
- 911 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity nerve growth factor receptor; Beta-nerve growth factor
- EC
- 2.7.10.1
- UniProt
- P04629, P01138
- Ligands
- NAG, NDG, BMA, MAN
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 347 | 7% helix, 33% strand | P04629 |
| E | Beta-nerve growth factor | protein | 108 | 4% helix, 60% strand | P01138 |
| F | Beta-nerve growth factor | protein | 109 | 4% helix, 63% strand | P01138 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies
- MAN · alpha-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.73 | 0.91 | 29 | empty |
| 2 | 238 | 0.72 | 0.87 | 37 | empty |
| 3 | 149 | 0.70 | 0.90 | 36 | empty |
| 4 | 60 | 0.69 | 0.96 | 15 | empty |
| 5 | 173 | 0.69 | 0.88 | 36 | empty |
Interfaces
5 interfaces between chains.
- E–F · 1687 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 816 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 801 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 376 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 375 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 2IFG · Structure of the extracellular segment of human TRKA in complex with nerve growth factor · the same entry in another collection · chain A against A, TM-score 1.00
- P01138 · AlphaFold monomer V2.0 prediction for beta-nerve growth factor (P01138) · a predicted model of the same protein · chain F against A, TM-score 0.85
- P04629 · AlphaFold monomer V2.0 prediction for high affinity nerve growth factor receptor (P04629) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 P04629
- Every structure of UniProt P01138
- Elsewhere: RCSB PDB 2IFG · PDBe 2IFG · UniProt P04629 · UniProt P01138
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