Research workbench
Variable lymphocyte receptor recognition of the immunodominant glycoprotein of bacillus anthracis spores
Analyse Variable lymphocyte receptor recognition of the immunodominant glycoprotein of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TWI
- Type
- protein
- Length
- 859 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bcla protein; Variable lymphocyte receptor B
- UniProt
- Q81JD7, A9Z0I5
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Bcla protein | protein | 136 | 0% helix, 60% strand | Q81JD7 |
| D | Variable lymphocyte receptor B | protein | 168 | 11% helix, 15% strand | A9Z0I5 |
| E | Variable lymphocyte receptor B | protein | 166 | 14% helix, 15% strand | A9Z0I5 |
| F | Variable lymphocyte receptor B | protein | 117 | 12% helix, 14% strand | A9Z0I5 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.72 | 0.99 | 19 | empty |
| 2 | 396 | 0.67 | 0.80 | 48 | empty |
| 3 | 277 | 0.54 | 0.76 | 33 | empty |
| 4 | 52 | 0.47 | 0.86 | 21 | empty |
| 5 | 151 | 0.45 | 0.76 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1049 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1048 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1034 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 587 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 555 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3TWI · Variable Lymphocyte Receptor Recognition of the Immunodominant Glycoprotein of Bacillus… · the same entry in another collection · chain E against E, 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 Q81JD7
- Every structure of UniProt A9Z0I5
- Elsewhere: RCSB PDB 3TWI · PDBe 3TWI · UniProt Q81JD7 · UniProt A9Z0I5
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