MolNFT v1 · #139279 · protein
Structural insights into the elevator-like mechanism of the SODIUM/CITRATE symporter cits
5XAT · Citrate-sodium symporter: “Structural insights into the elevator-like mechanism of the SODIUM/CITRATE symporter cits”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.84). MolNFT v1 #139279 on GenesisL1: 3D…
- PDB
- 5XAT
- Type
- protein
- Length
- 1,641 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate-sodium symporter
- UniProt
- P31602
- Ligands
- NA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 79% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate-sodium symporter | protein | 418 | 78% helix, 2% strand | P31602 |
| B | Citrate-sodium symporter | protein | 409 | 79% helix, 1% strand | P31602 |
| C | Citrate-sodium symporter | protein | 408 | 79% helix, 1% strand | P31602 |
| D | Citrate-sodium symporter | protein | 406 | 81% helix, 1% strand | P31602 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, D
- FLC · Citrate anion · additive · 3 copies · chains A, B, C
- BOG · octyl beta-D-glucopyranoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.84 | 0.97 | 21 | empty |
| 2 | 172 | 0.83 | 0.96 | 22 | empty |
| 3 | 442 | 0.72 | 0.82 | 52 | empty |
| 4 | 393 | 0.70 | 0.81 | 51 | empty |
| 5 | 549 | 0.69 | 0.78 | 68 | BOG |
Interfaces
4 interfaces between chains.
- A–D · 2914 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2866 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 135 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XAT · Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS · the same entry in another collection · chain D against D, TM-score 1.00
- P31602 · AlphaFold monomer V2.0 prediction for citrate-sodium symporter (P31602) · a predicted model of the same protein · chain D 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 P31602
- Elsewhere: RCSB PDB 5XAT · PDBe 5XAT · UniProt P31602
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