Research workbench
Structure and function of the divalent ANION/NA+ symporter from vibrio cholerae and a humanized variant
Analyse Structure and function of the divalent ANION/NA+ symporter from vibrio cholerae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ULE
- Type
- protein
- Length
- 1,780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transporter, nadc family
- UniProt
- Q9KNE0
- Ligands
- NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transporter, nadc family | protein | 445 | 74% helix, 0% strand | Q9KNE0 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 4 copies · chains A, B, C, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.82 | 0.99 | 16 | empty |
| 2 | 119 | 0.81 | 0.98 | 16 | empty |
| 3 | 51 | 0.68 | 0.96 | 12 | empty |
| 4 | 445 | 0.67 | 0.79 | 45 | empty |
| 5 | 428 | 0.67 | 0.80 | 55 | SIN |
Interfaces
4 interfaces between chains.
- C–D · 2144 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2129 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 353 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 91 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ULE · Structure and function of the divalent anion/Na+ symporter from Vibrio cholerae and a… · the same entry in another collection · chain A against A, 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 5ULE · PDBe 5ULE · UniProt Q9KNE0
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