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High resolution crystal structure of glucose complexed periplasmic glucose binding protein (ppgbp) from P. putida CSV86
Analyse High resolution crystal structure of glucose complexed periplasmic glucose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DVI
- Type
- protein
- Length
- 792 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Binding protein component of ABC sugar transporter
- UniProt
- H7BRJ8
- Ligands
- BGC, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Binding protein component of ABC sugar transporter | protein | 396 | 52% helix, 14% strand | H7BRJ8 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.78 | 0.80 | 77 | SO4 |
| 2 | 222 | 0.51 | 0.76 | 33 | empty |
| 3 | 103 | 0.45 | 0.78 | 15 | GOL |
| 4 | 129 | 0.45 | 0.77 | 22 | empty |
| 5 | 77 | 0.38 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DVI · High resolution crystal Structure of glucose complexed periplasmic glucose binding… · 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 H7BRJ8
- Elsewhere: RCSB PDB 5DVI · PDBe 5DVI · UniProt H7BRJ8
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