MolNFT v1 · #160681 · protein
Sbp rafe in complex with stachyose
6PRG · ABC transporter sugar-binding protein: “Sbp rafe in complex with stachyose”. X-ray diffraction, 3 ligands (GLA, GLC, FRU), 6 pockets (best druggability 0.78). MolNFT v1 #160681 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6PRG
- Type
- protein
- Length
- 772 residues
- Chains
- 2
- 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
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ABC transporter sugar-binding protein | protein | 386 | 47% helix, 16% strand | A0A0E8ZWG6 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- CIT · Citric acid · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.78 | 0.84 | 86 | EDO |
| 2 | 471 | 0.72 | 0.81 | 35 | GLC, GLA, FRU |
| 3 | 490 | 0.71 | 0.81 | 37 | GLC, GLA, FRU |
| 4 | 107 | 0.54 | 0.83 | 22 | empty |
| 5 | 127 | 0.54 | 0.82 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 623 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6PRG · SBP RafE in complex with stachyose · 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 6PRG · PDBe 6PRG · UniProt A0A0E8ZWG6
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