MolNFT v1 · #59725 · protein
Apo and ligand-bound form of a thermophilic GLUCOSE/XYLOSE binding protein
3C6Q · Sugar ABC transporter, periplasmic sugar-binding protein: “Apo and ligand-bound form of a thermophilic GLUCOSE/XYLOSE binding protein”. X-ray diffraction, 1 ligand (XYP), 7 pockets (best druggability 0.63). MolNFT v1 #59725 on…
- PDB
- 3C6Q
- Type
- protein
- Length
- 1,220 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter, periplasmic sugar-binding protein
- UniProt
- Q9WXW9
- Ligands
- XYP
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 305 | 44% helix, 22% strand | Q9WXW9 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.63 | 0.76 | 50 | empty |
| 2 | 432 | 0.62 | 0.76 | 49 | empty |
| 3 | 254 | 0.52 | 0.75 | 36 | empty |
| 4 | 168 | 0.43 | 0.74 | 20 | empty |
| 5 | 74 | 0.40 | 0.79 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–C · 865 Ų buried · 3 hydrogen bonds · protein-protein
- B–A · 209 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 151 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 73 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 39 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3C6Q · Apo and ligand-bound form of a thermophilic glucose/xylose binding protein · the same entry in another collection · chain B against B, 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 Q9WXW9
- Elsewhere: RCSB PDB 3C6Q · PDBe 3C6Q · UniProt Q9WXW9
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