MolNFT v1 · #117014 · protein
Crystal structure of galactose complexed periplasmic glucose binding protein (ppgbp) from P. putida CSV86
5DVJ · Binding protein component of ABC sugar transporter: “Crystal structure of galactose complexed periplasmic glucose binding protein (ppgbp) from P. putida CSV86”. X-ray diffraction, 2 ligands (GAL, SO4), 7 pockets (best druggability…
- 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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