MolNFT v1 · #122248 · protein
Structure of the spx domain of the human phosphate transporter XPR1 in complex with a sulfate ion
5IJH · Xenotropic and polytropic retrovirus receptor 1: “Structure of the spx domain of the human phosphate transporter XPR1 in complex with a sulfate ion”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.58). MolNFT v1…
- PDB
- 5IJH
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xenotropic and polytropic retrovirus receptor 1
- UniProt
- Q9UBH6
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 83% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xenotropic and polytropic retrovirus receptor 1 | protein | 181 | 82% helix, 0% strand | Q9UBH6 |
| B | Xenotropic and polytropic retrovirus receptor 1 | protein | 184 | 83% helix, 1% strand | Q9UBH6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.58 | 0.87 | 35 | empty |
| 2 | 263 | 0.55 | 0.77 | 30 | empty |
| 3 | 53 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1723 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5IJH · Structure of the SPX domain of the human phosphate transporter XPR1 in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBH6 · AlphaFold monomer V2.0 prediction for xenotropic and polytropic retrovirus receptor 1… · a predicted model of the same protein · chain B against A, TM-score 0.90
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 Q9UBH6
- Elsewhere: RCSB PDB 5IJH · PDBe 5IJH · UniProt Q9UBH6
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