MolNFT v1 · #136193 · protein
Structure and function of the divalent ANION/NA+ symporter from vibrio cholerae and a humanized variant
5ULD · Transporter, nadc family: “Structure and function of the divalent ANION/NA+ symporter from vibrio cholerae and a humanized variant”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.82). MolNFT v1 #136193 on…
- PDB
- 5ULD
- 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
- CIT · Citric 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.82 | 0.99 | 16 | empty |
| 2 | 121 | 0.82 | 0.99 | 16 | empty |
| 3 | 866 | 0.77 | 0.80 | 89 | CIT |
| 4 | 870 | 0.75 | 0.78 | 103 | CIT |
| 5 | 580 | 0.71 | 0.79 | 64 | CIT |
Interfaces
4 interfaces between chains.
- C–D · 2142 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2133 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 473 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ULD · 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 5ULD · PDBe 5ULD · UniProt Q9KNE0
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