Research workbench
Crystal structure of the dnak C-terminus with the inhibitor pet-16
Analyse Crystal structure of the dnak C-terminus with the inhibitor pet-16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R5G
- Type
- protein
- Length
- 427 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak
- UniProt
- P0A6Y8
- Ligands
- 3JE
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein dnak | protein | 218 | 35% helix, 23% strand | P0A6Y8 |
| B | Chaperone protein dnak | protein | 209 | 34% helix, 27% strand | P0A6Y8 |
Ligands and binding sites
- 3JE · triphenyl(phenylethynyl)phosphonium · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.59 | 0.77 | 37 | empty |
| 2 | 101 | 0.44 | 0.78 | 16 | empty |
| 3 | 88 | 0.41 | 0.78 | 15 | empty |
| 4 | 58 | 0.39 | 0.80 | 15 | 3JE |
| 5 | 69 | 0.35 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 681 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4R5G · Crystal structure of the DnaK C-terminus with the inhibitor PET-16 · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6Y8 · AlphaFold monomer V2.0 prediction for chaperone protein dnak (P0A6Y8) · a predicted model of the same protein · chain B against A, TM-score 0.48
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 P0A6Y8
- Elsewhere: RCSB PDB 4R5G · PDBe 4R5G · UniProt P0A6Y8
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