MolNFT v1 · #59774 · protein
Crystal structure of trka domain of putative glutathione-regulated potassium-efflux kefb from vibrio parahaemolyticus
3C85 · Putative glutathione-regulated potassium-efflux system…: “Crystal structure of trka domain of putative glutathione-regulated potassium-efflux kefb from vibrio…”. X-ray diffraction, 2 ligands (AMP, SO4), 10 pockets (best druggability…
- PDB
- 3C85
- Type
- protein
- Length
- 552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glutathione-regulated potassium-efflux system protein kefb
- UniProt
- Q87RG9
- Ligands
- AMP, SO4
- Pockets
- 10 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative glutathione-regulated potassium-efflux system protein kefb | protein | 150 | 45% helix, 19% strand | Q87RG9 |
| B | Putative glutathione-regulated potassium-efflux system protein kefb | protein | 144 | 44% helix, 19% strand | Q87RG9 |
| C | Putative glutathione-regulated potassium-efflux system protein kefb | protein | 146 | 47% helix, 18% strand | Q87RG9 |
| D | Putative glutathione-regulated potassium-efflux system protein kefb | protein | 112 | 43% helix, 23% strand | Q87RG9 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains B, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.55 | 0.83 | 21 | empty |
| 2 | 128 | 0.55 | 0.82 | 18 | empty |
| 3 | 152 | 0.49 | 0.78 | 29 | empty |
| 4 | 89 | 0.47 | 0.81 | 21 | empty |
| 5 | 175 | 0.46 | 0.75 | 25 | AMP |
Interfaces
2 interfaces between chains.
- A–C · 2286 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1939 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3C85 · Crystal structure of TrkA domain of putative glutathione-regulated potassium-efflux KefB… · 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 Q87RG9
- Elsewhere: RCSB PDB 3C85 · PDBe 3C85 · UniProt Q87RG9
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