MolNFT v1 · #97216 · protein
Recognition of the thomsen-friedenreich antigen by a lamprey variable lymphocyte receptor
4K79: “Recognition of the thomsen-friedenreich antigen by a lamprey variable lymphocyte receptor”. X-ray diffraction, 2 ligands (A2G, GAL), 5 pockets (best druggability 0.82). MolNFT v1 #97216 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4K79
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variable lymphocyte receptor
- UniProt
- K0IE77
- Ligands
- A2G, GAL
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Variable lymphocyte receptor | protein | 218 | 10% helix, 16% strand | K0IE77 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 3 copies · chains B, C, D
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.82 | 0.86 | 96 | empty |
| 2 | 180 | 0.54 | 0.79 | 22 | empty |
| 3 | 57 | 0.50 | 0.87 | 18 | empty |
| 4 | 62 | 0.50 | 0.86 | 17 | empty |
| 5 | 73 | 0.46 | 0.82 | 18 | A2G, GAL |
Interfaces
6 interfaces between chains.
- C–D · 810 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 785 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 331 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 319 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 250 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 4K79 · Recognition of the Thomsen-Friedenreich Antigen by a Lamprey Variable Lymphocyte Receptor · 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 K0IE77
- Elsewhere: RCSB PDB 4K79 · PDBe 4K79 · UniProt K0IE77
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