MolNFT v1 · #112980 · protein
Crystal structure of the sodium-dependent citrate symporter secits form salmonella enterica.
5A1S · Citrate-sodium symporter: “Crystal structure of the sodium-dependent citrate symporter secits form salmonella enterica.”. X-ray diffraction, 3 ligands (PTY, NA, CL), 20 pockets (best druggability 0.82). MolNFT v1 #112980 on…
- PDB
- 5A1S
- Type
- protein
- Length
- 1,721 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate-sodium symporter
- UniProt
- G4BX92
- Ligands
- PTY, NA, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 76% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate-sodium symporter | protein | 433 | 77% helix, 2% strand | G4BX92 |
| B | Citrate-sodium symporter | protein | 426 | 76% helix, 1% strand | G4BX92 |
| C | Citrate-sodium symporter | protein | 428 | 75% helix, 3% strand | G4BX92 |
| D | Citrate-sodium symporter | protein | 434 | 76% helix, 1% strand | G4BX92 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · chains A, C
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, D, C
- FLC · Citrate anion · additive · 7 copies · chains A, B, C, D
- BOG · octyl beta-D-glucopyranoside · additive · 5 copies · chains A, C, D
- UND · Undecane · additive · 2 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.82 | 0.94 | 27 | UND |
| 2 | 213 | 0.80 | 0.92 | 28 | UND |
| 3 | 976 | 0.78 | 0.80 | 80 | FLC, CL |
| 4 | 518 | 0.73 | 0.81 | 49 | FLC |
| 5 | 490 | 0.73 | 0.82 | 46 | FLC |
Interfaces
4 interfaces between chains.
- C–D · 3161 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2949 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 352 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 302 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5A1S · Crystal structure of the sodium-dependent citrate symporter SeCitS form Salmonella… · the same entry in another collection · chain D against D, TM-score 1.00
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 G4BX92
- Elsewhere: RCSB PDB 5A1S · PDBe 5A1S · UniProt G4BX92
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