Research workbench
Crystal structure from a domain (Thr161-F265) from fructose-specific iiabc component (Pts system) from Borrelia burgdorferi
Analyse Crystal structure from a domain (Thr161-F265) from fructose-specific iiabc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DLE
- Type
- protein
- Length
- 416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.55
- Source
- Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680)
- Molecule
- Pts system, fructose-specific iiabc component
- UniProt
- O51369
- Ligands
- CL
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · resolution 1.55 · 1 distinct chain · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pts system, fructose-specific iiabc component | protein | 104 | 38% helix, 27% strand | O51369 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.55 | 0.81 | 29 | empty |
| 2 | 122 | 0.44 | 0.77 | 28 | empty |
| 3 | 71 | 0.33 | 0.76 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–C · 555 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 544 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 372 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 370 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 131 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DLE · Crystal structure from a domain (THR161-F265) from fructose-specific iiabc component (pts… · 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 O51369
- Elsewhere: RCSB PDB 5DLE · PDBe 5DLE · UniProt O51369
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.