MolNFT v1 · #13354 · protein
Crystal structure of lyme disease variable surface antigen vlse of borrelia burgdorferi
1L8W · VLSE1: “Crystal structure of lyme disease variable surface antigen vlse of borrelia burgdorferi”. X-ray diffraction, 12 pockets (best druggability 0.83). MolNFT v1 #13354 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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