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The ABC transporter associated binding protein from B. animalis subsp. lactis Bl-04 in complex with beta-1,6-galactobiose
Analyse The ABC transporter associated binding protein from B. animalis subsp. lactis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H0H
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.39
- Source
- Bifidobacterium animalis subsp. lactis Bl-04
- Molecule
- Probable solute binding protein of ABC transporter system for sugars
- UniProt
- B8DWA9
- Ligands
- GAL, GLA
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.39 · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable solute binding protein of ABC transporter system for sugars | protein | 410 | 45% helix, 17% strand | B8DWA9 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.79 | 0.81 | 116 | GAL, GLA |
| 2 | 300 | 0.75 | 0.88 | 46 | GAL, GLA |
| 3 | 310 | 0.59 | 0.78 | 43 | empty |
| 4 | 253 | 0.51 | 0.75 | 32 | empty |
| 5 | 153 | 0.47 | 0.77 | 38 | PG4 |
Interfaces
1 interface between chains.
- A–B · 858 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6H0H · The ABC transporter associated binding protein from B. animalis subsp. lactis bl-04 in… · 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 B8DWA9
- Elsewhere: RCSB PDB 6H0H · PDBe 6H0H · UniProt B8DWA9
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