Research workbench
Crystal structure of galactose complexed periplasmic glucose binding protein (ppgbp) from P. putida CSV86
Analyse Crystal structure of galactose complexed periplasmic glucose binding protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DVJ
- 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
- GAL, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Binding protein component of ABC sugar transporter | protein | 396 | 51% helix, 14% strand | H7BRJ8 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 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 | 994 | 0.82 | 0.83 | 71 | empty |
| 2 | 254 | 0.54 | 0.77 | 32 | empty |
| 3 | 133 | 0.44 | 0.77 | 23 | empty |
| 4 | 111 | 0.43 | 0.77 | 17 | empty |
| 5 | 84 | 0.40 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1056 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5DVJ · Crystal structure of galactose complexed periplasmic glucose binding protein (ppGBP) from… · 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 5DVJ · PDBe 5DVJ · UniProt H7BRJ8
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