MolNFT v1 · #117011 · protein
Crystal structure of unliganded periplasmic glucose binding protein (ppgbp) from P. putida CSV86
5DVF · Binding protein component of ABC sugar transporter: “Crystal structure of unliganded periplasmic glucose binding protein (ppgbp) from P. putida CSV86”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.69). MolNFT…
- PDB
- 5DVF
- Type
- protein
- Length
- 778 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
- SO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Binding protein component of ABC sugar transporter | protein | 389 | 51% helix, 16% strand | H7BRJ8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.69 | 0.77 | 76 | empty |
| 2 | 275 | 0.65 | 0.82 | 30 | empty |
| 3 | 311 | 0.65 | 0.81 | 32 | empty |
| 4 | 60 | 0.43 | 0.82 | 17 | empty |
| 5 | 86 | 0.43 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 632 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5DVF · Crystal structure of unliganded periplasmic glucose binding protein (ppGBP) from P.… · 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 5DVF · PDBe 5DVF · UniProt H7BRJ8
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