Research workbench
Sbp rafe in complex with verbascose
Analyse Sbp rafe in complex with verbascose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PRE
- Type
- protein
- Length
- 1,540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter sugar-binding protein
- UniProt
- A0A0E8ZWG6
- Ligands
- GLA, GLC, FRU
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ABC transporter sugar-binding protein | protein | 386 | 45% helix, 15% strand | A0A0E8ZWG6 |
| B, D | ABC transporter sugar-binding protein | protein | 384 | 45% helix, 16% strand | A0A0E8ZWG6 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 12 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- FRU · beta-D-fructofuranose · sugar · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.81 | 0.82 | 133 | empty |
| 2 | 631 | 0.79 | 0.85 | 96 | EDO |
| 3 | 432 | 0.76 | 0.85 | 34 | GLC, GLA |
| 4 | 437 | 0.73 | 0.83 | 41 | GLC, GLA |
| 5 | 421 | 0.73 | 0.83 | 36 | GLC, GLA |
Interfaces
3 interfaces between chains.
- A–B · 668 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 647 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 171 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6PRE · SBP RafE in complex with verbascose · 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 A0A0E8ZWG6
- Elsewhere: RCSB PDB 6PRE · PDBe 6PRE · UniProt A0A0E8ZWG6
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