Research workbench
Crystal structure of lyme disease variable surface antigen vlse of borrelia burgdorferi
Analyse Crystal structure of lyme disease variable surface antigen vlse of borrelia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L8W
- Type
- protein
- Length
- 1,141 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VLSE1
- UniProt
- O06878
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VLSE1 | protein | 271 | 61% helix, 2% strand | O06878 |
| B | VLSE1 | protein | 296 | 60% helix, 2% strand | O06878 |
| C | VLSE1 | protein | 274 | 63% helix, 2% strand | O06878 |
| D | VLSE1 | protein | 300 | 61% helix, 1% strand | O06878 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.83 | 0.85 | 108 | empty |
| 2 | 665 | 0.74 | 0.80 | 61 | empty |
| 3 | 381 | 0.73 | 0.84 | 60 | empty |
| 4 | 56 | 0.55 | 0.89 | 17 | empty |
| 5 | 128 | 0.40 | 0.75 | 29 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1950 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1537 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 366 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 357 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 81 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1L8W · Crystal Structure of Lyme Disease Variable Surface Antigen VlsE of Borrelia burgdorferi · 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 O06878
- Elsewhere: RCSB PDB 1L8W · PDBe 1L8W · UniProt O06878
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