MolNFT v1 · #110310 · protein
Structure of a variable lymphocyte receptor-like protein BF66946 from branchiostoma floridae
4XSQ: “Structure of a variable lymphocyte receptor-like protein BF66946 from branchiostoma floridae”. X-ray diffraction, 5 pockets (best druggability 0.74). MolNFT v1 #110310 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XSQ
- Type
- protein
- Length
- 354 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variable lymphocyte receptor-like protein BF66946
- UniProt
- C3YZ59
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Variable lymphocyte receptor-like protein BF66946 | protein | 174 | 20% helix, 20% strand | C3YZ59 |
| B | Variable lymphocyte receptor-like protein BF66946 | protein | 180 | 18% helix, 18% strand | C3YZ59 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.74 | 0.77 | 78 | empty |
| 2 | 91 | 0.47 | 0.81 | 31 | empty |
| 3 | 53 | 0.32 | 0.77 | 14 | EDO |
| 4 | 52 | 0.30 | 0.76 | 13 | empty |
| 5 | 53 | 0.26 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 620 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified, 8 disulfide (engineered, disulfide).
Compared structures
- 4XSQ · Structure of a variable lymphocyte receptor-like protein Bf66946 from Branchiostoma… · the same entry in another collection · chain A against A, TM-score 1.00
- C3YZ59 · AlphaFold monomer V2.0 prediction for leucine-rich repeat-containing protein BF66946… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 C3YZ59
- Elsewhere: RCSB PDB 4XSQ · PDBe 4XSQ · UniProt C3YZ59
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