MolNFT v1 · #106200 · protein
Crystal structure of carbohydrate transporter A0QYB3 from mycobacterium smegmatis str. MC2 155, target efi-510969, in complex with xylitol
4RS3 · ABC transporter, carbohydrate uptake transporter-2 (CUT2)…: “Crystal structure of carbohydrate transporter A0QYB3 from mycobacterium smegmatis str. MC2 155, target…”. X-ray diffraction, 3 ligands (XYL, ZN, CL), 1 pocket (best…
- PDB
- 4RS3
- Type
- protein
- Length
- 315 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic…
- EC
- 3.6.3.17
- UniProt
- A0QYB3
- Ligands
- XYL, ZN, CL
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein (EC 3.6.3.17) | protein | 315 | 49% helix, 18% strand | A0QYB3 |
Ligands and binding sites
- XYL · Xylitol · ligand · chains A
- ZN · Zinc ion · metal · 11 copies · chains A
- CL · Chloride ion · ion · 16 copies · chains A
- IMD · Imidazole · additive · 4 copies · chains A
- ACT · Acetate ion · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.64 | 0.92 | 27 | XYL |
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4RS3 · Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str.… · the same entry in another collection · chain A against A, TM-score 1.00
- A0QYB3 · AlphaFold monomer V2.0 prediction for xylitol-binding protein (A0QYB3) · a predicted model of the same protein · 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 A0QYB3
- Elsewhere: RCSB PDB 4RS3 · PDBe 4RS3 · UniProt A0QYB3
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