Research workbench
Ngf in complex with domain 5 of the trka receptor
Analyse Ngf in complex with domain 5 of the trka receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WWW
- Type
- protein
- Length
- 419 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (nerve growth factor); Protein (trka receptor)
- UniProt
- P01138, P04629
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | Protein (nerve growth factor) | protein | 108 | 4% helix, 59% strand | P01138 |
| W | Protein (nerve growth factor) | protein | 109 | 4% helix, 61% strand | P01138 |
| X, Y | Protein (trka receptor) | protein | 101 | 3% helix, 56% strand | P04629 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.72 | 0.91 | 35 | empty |
| 2 | 139 | 0.71 | 0.91 | 34 | empty |
| 3 | 265 | 0.66 | 0.82 | 47 | empty |
| 4 | 87 | 0.50 | 0.83 | 20 | empty |
| 5 | 85 | 0.46 | 0.81 | 21 | empty |
Interfaces
5 interfaces between chains.
- V–W · 1728 Ų buried · 13 hydrogen bonds · protein-protein
- W–X · 827 Ų buried · 8 hydrogen bonds · protein-protein
- V–Y · 802 Ų buried · 6 hydrogen bonds · protein-protein
- V–X · 406 Ų buried · 5 hydrogen bonds · protein-protein
- W–Y · 396 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1WWW · Ngf in complex with domain 5 of the trka receptor · the same entry in another collection · chain V against V, TM-score 1.00
- P04629 · AlphaFold monomer V2.0 prediction for high affinity nerve growth factor receptor (P04629) · a predicted model of the same protein · chain X against A, TM-score 0.98
- P01138 · AlphaFold monomer V2.0 prediction for beta-nerve growth factor (P01138) · a predicted model of the same protein · chain W against A, TM-score 0.85
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 P04629
- Elsewhere: RCSB PDB 1WWW · PDBe 1WWW · UniProt P01138 · UniProt P04629
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