Research workbench
Thermus thermophilus Glucose/Galactose Binding Protein With Bound Glucose
Analyse Thermus thermophilus Glucose/Galactose Binding Protein With Bound Glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B3B
- Type
- protein
- Length
- 2,351 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Thermus thermophilus HB27
- Molecule
- glucose-binding protein
- UniProt
- Q72KX2
- Ligands
- GLC, BGC
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.95 · 2 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | glucose-binding protein | protein | 392 | 53% helix, 15% strand | Q72KX2 |
| B | glucose-binding protein | protein | 391 | 52% helix, 15% strand | Q72KX2 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, E, F
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.81 | 0.87 | 100 | empty |
| 2 | 1098 | 0.81 | 0.82 | 102 | empty |
| 3 | 482 | 0.79 | 0.86 | 58 | empty |
| 4 | 959 | 0.78 | 0.80 | 128 | empty |
| 5 | 1155 | 0.75 | 0.78 | 87 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1014 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 975 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 784 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 543 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 330 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2B3B · Thermus thermophilus GLUCOSE/GALACTOSE binding protein with bound glucose · 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 Q72KX2
- Elsewhere: RCSB PDB 2B3B · PDBe 2B3B · UniProt Q72KX2
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