Research workbench
Crystal structure of a bacterial DICARBOXYLATE/SODIUM symporter
Analyse Crystal structure of a bacterial DICARBOXYLATE/SODIUM symporter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F35
- Type
- protein
- Length
- 1,708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transporter, nadc family
- UniProt
- Q9KNE0
- Ligands
- BNG, NA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Transporter, nadc family | protein | 430 | 72% helix, 1% strand | Q9KNE0 |
| B | Transporter, nadc family | protein | 414 | 75% helix, 0% strand | Q9KNE0 |
| A | Transporter, nadc family | protein | 434 | 71% helix, 0% strand | Q9KNE0 |
| C | Transporter, nadc family | protein | 430 | 72% helix, 0% strand | Q9KNE0 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 3 copies · chains D, B, C
- NA · Sodium ion · metal · 4 copies · chains D, B, A, C
- CIT · Citric acid · additive · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.83 | 0.98 | 16 | empty |
| 2 | 131 | 0.83 | 0.99 | 16 | empty |
| 3 | 896 | 0.71 | 0.76 | 93 | empty |
| 4 | 349 | 0.70 | 0.82 | 54 | empty |
| 5 | 362 | 0.66 | 0.80 | 42 | CIT |
Interfaces
4 interfaces between chains.
- B–A · 1953 Ų buried · 12 hydrogen bonds · protein-protein
- D–C · 1936 Ų buried · 12 hydrogen bonds · protein-protein
- D–A · 93 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 87 modified (engineered).
Compared structures
- 4F35 · Crystal Structure of a bacterial dicarboxylate/sodium symporter · 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 Q9KNE0
- Elsewhere: RCSB PDB 4F35 · PDBe 4F35 · UniProt Q9KNE0
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