MolNFT v1 · #92560 · protein
The structure of the mfs (major facilitator superfamily) PROTON:XYLOSE symporter xyle bound to D-xylose
4GBY · D-xylose-proton symporter: “The structure of the mfs (major facilitator superfamily) PROTON:XYLOSE symporter xyle bound to D-xylose”. X-ray diffraction, 2 ligands (BNG, XYP), 5 pockets (best druggability 0.77). MolNFT v1 #92560 on…
- PDB
- 4GBY
- Type
- protein
- Length
- 475 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-xylose-proton symporter
- UniProt
- P0AGF4
- Ligands
- BNG, XYP
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-xylose-proton symporter | protein | 475 | 81% helix, 0% strand | P0AGF4 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 4 copies · chains A
- XYP · beta-D-xylopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.77 | 0.81 | 63 | empty |
| 2 | 71 | 0.74 | 0.98 | 18 | XYP |
| 3 | 170 | 0.59 | 0.82 | 25 | BNG |
| 4 | 84 | 0.45 | 0.80 | 19 | empty |
| 5 | 78 | 0.39 | 0.77 | 16 | empty |
Compared structures
- 4GBY · The structure of the MFS (major facilitator superfamily) proton:xylose symporter XylE… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AGF4 · AlphaFold monomer V2.0 prediction for D-xylose-proton symporter (P0AGF4) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P0AGF4
- Elsewhere: RCSB PDB 4GBY · PDBe 4GBY · UniProt P0AGF4
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