Research workbench
Structural insights into the elevator-like mechanism of the SODIUM/CITRATE symporter cits
Analyse Structural insights into the elevator-like mechanism of the SODIUM/CITRATE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X9R
- Type
- protein
- Length
- 825 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate-sodium symporter
- UniProt
- P31602
- Ligands
- BGC
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate-sodium symporter | protein | 416 | 76% helix, 1% strand | P31602 |
| B | Citrate-sodium symporter | protein | 409 | 78% helix, 1% strand | P31602 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- FLC · Citrate anion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.85 | 0.95 | 31 | empty |
| 2 | 465 | 0.69 | 0.79 | 58 | BGC |
| 3 | 454 | 0.68 | 0.79 | 56 | BGC |
| 4 | 219 | 0.50 | 0.75 | 34 | FLC |
| 5 | 148 | 0.44 | 0.76 | 20 | FLC |
Interfaces
1 interface between chains.
- A–B · 2868 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5X9R · Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS · the same entry in another collection · chain A against A, TM-score 1.00
- P31602 · AlphaFold monomer V2.0 prediction for citrate-sodium symporter (P31602) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 P31602
- Elsewhere: RCSB PDB 5X9R · PDBe 5X9R · UniProt P31602
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