Research workbench
Raffinose and panose binding protein from bifidobacterium animalis subsp. lactis bl-04, bound with raffinose, selenomethionine derivative
Analyse Raffinose and panose binding protein from bifidobacterium animalis subsp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZZA
- Type
- protein
- Length
- 732 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar binding protein of ABC transporter system
- UniProt
- C6A9Y6
- Ligands
- FRU, GLC, GLA
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar binding protein of ABC transporter system | protein | 364 | 49% helix, 14% strand | C6A9Y6 |
| B | Sugar binding protein of ABC transporter system | protein | 368 | 51% helix, 13% strand | C6A9Y6 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.73 | 0.78 | 94 | empty |
| 2 | 297 | 0.63 | 0.80 | 35 | FRU, GLC, GLA |
| 3 | 306 | 0.62 | 0.79 | 30 | FRU, GLC, GLA |
| 4 | 67 | 0.37 | 0.78 | 15 | empty |
| 5 | 66 | 0.36 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 482 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4ZZA · Raffinose and panose binding protein from Bifidobacterium animalis subsp. lactis Bl-04… · 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 C6A9Y6
- Elsewhere: RCSB PDB 4ZZA · PDBe 4ZZA · UniProt C6A9Y6
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