MolNFT v1 · #96106 · protein
Inward open conformation of the xylose transporter xyle from E. COLI
4JA4 · D-xylose-proton symporter: “Inward open conformation of the xylose transporter xyle from E. COLI”. X-ray diffraction, 1 ligand (CD), 15 pockets (best druggability 0.82). MolNFT v1 #96106 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4JA4
- Type
- protein
- Length
- 1,317 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-xylose-proton symporter
- UniProt
- P0AGF4
- Ligands
- CD
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-xylose-proton symporter | protein | 442 | 66% helix, 0% strand | P0AGF4 |
| B | D-xylose-proton symporter | protein | 439 | 67% helix, 0% strand | P0AGF4 |
| C | D-xylose-proton symporter | protein | 436 | 67% helix, 0% strand | P0AGF4 |
Ligands and binding sites
- CD · Cadmium ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.82 | 0.83 | 86 | empty |
| 2 | 983 | 0.80 | 0.82 | 79 | empty |
| 3 | 672 | 0.80 | 0.84 | 58 | empty |
| 4 | 891 | 0.80 | 0.82 | 69 | empty |
| 5 | 154 | 0.61 | 0.84 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–C · 572 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 571 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 570 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4JA4 · Inward open conformation of the xylose transporter XylE from E. coli · 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 C against A, TM-score 0.99
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 4JA4 · PDBe 4JA4 · UniProt P0AGF4
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