MolNFT v1 · #182773 · protein
Trka ecd complex with designed miniprotein ligand
7N3T · High affinity nerve growth factor receptor: “Trka ecd complex with designed miniprotein ligand”. X-ray diffraction, 3 ligands (NAG, BMA, SO4), 1 pocket (best druggability 0.63). MolNFT v1 #182773 on GenesisL1: 3D structure, binding…
- PDB
- 7N3T
- Type
- protein
- Length
- 813 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity nerve growth factor receptor; Designed trka-binding miniprotein
- EC
- 2.7.10.1
- UniProt
- P04629
- Ligands
- NAG, BMA, SO4
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 348 | 12% helix, 39% strand | P04629 |
| B | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 346 | 12% helix, 40% strand | P04629 |
| C | Designed trka-binding miniprotein | protein | 60 | 83% helix, 0% strand | — |
| D | Designed trka-binding miniprotein | protein | 59 | 83% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 10 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.63 | 0.80 | 35 | empty |
Interfaces
4 interfaces between chains.
- A–C · 787 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 779 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 346 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 184 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 7N3T · TrkA ECD complex with designed miniprotein ligand · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 7N3T · PDBe 7N3T · UniProt P04629
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.