Research workbench
Structure of the extracellular segment of human trka in complex with nerve growth factor
Analyse Structure of the extracellular segment of human trka in complex with nerve… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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