Research workbench
Recognition of the bg-H antigen by a lamprey variable lymphocyte receptor
Analyse Recognition of the bg-H antigen by a lamprey variable lymphocyte receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K5U
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variable lymphocyte receptor
- UniProt
- K0IE77
- Ligands
- GAL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Variable lymphocyte receptor | protein | 218 | 10% helix, 16% strand | K0IE77 |
| C, D | Variable lymphocyte receptor | protein | 217 | 10% helix, 16% strand | K0IE77 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.74 | 0.80 | 68 | GAL |
| 2 | 520 | 0.71 | 0.80 | 59 | GAL |
| 3 | 235 | 0.56 | 0.79 | 43 | empty |
| 4 | 54 | 0.43 | 0.83 | 16 | GAL |
| 5 | 110 | 0.42 | 0.77 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–D · 823 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 805 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 417 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 416 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 173 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 4K5U · Recognition of the BG-H Antigen by a Lamprey Variable Lymphocyte Receptor · the same entry in another collection · chain B against B, 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 4K5U · PDBe 4K5U · UniProt K0IE77
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