MolNFT v1 · #87245 · protein
Structure and allostery in toll-spatzle recognition
4BV4 · Protein spaetzle C-106: “Structure and allostery in toll-spatzle recognition”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 7 pockets (best druggability 0.67). MolNFT v1 #87245 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4BV4
- Type
- protein
- Length
- 574 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein spaetzle C-106; Protein toll, variable lymphocyte receptor B chimera
- UniProt
- P48607, P08953, Q4G1L2
- Ligands
- NAG, BMA, MAN
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Protein spaetzle C-106 | protein | 66 | 5% helix, 55% strand | P48607 |
| M | Protein spaetzle C-106 | protein | 68 | 0% helix, 56% strand | P48607 |
| R | Protein toll, variable lymphocyte receptor B chimera | protein | 440 | 11% helix, 19% strand | P08953, Q4G1L2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains R
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains R
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.67 | 0.87 | 29 | empty |
| 2 | 291 | 0.65 | 0.82 | 40 | empty |
| 3 | 246 | 0.64 | 0.82 | 31 | empty |
| 4 | 219 | 0.50 | 0.76 | 26 | empty |
| 5 | 57 | 0.46 | 0.84 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–M · 1442 Ų buried · 27 hydrogen bonds · protein-protein
- M–R · 1257 Ų buried · 25 hydrogen bonds · protein-protein
- L–R · 580 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4BV4 · Structure and allostery in Toll-Spatzle recognition · the same entry in another collection · chain L against L, TM-score 1.00
- P08953 · AlphaFold monomer V2.0 prediction for protein toll (P08953) · a predicted model of the same protein · chain R against A, TM-score 0.95
- P48607 · AlphaFold monomer V2.0 prediction for protein spaetzle (P48607) · a predicted model of the same protein · chain L against A, TM-score 0.88
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 P48607
- Every structure of UniProt P08953
- Every structure of UniProt Q4G1L2
- Elsewhere: RCSB PDB 4BV4 · PDBe 4BV4 · UniProt P48607 · UniProt P08953 · UniProt Q4G1L2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.