Research workbench
Structure of full-length dnak with bound J-domain
Analyse Structure of full-length dnak with bound J-domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NRO
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak; Chaperone protein dnaj
- UniProt
- P0A6Y8, P08622
- Ligands
- ATP, MG
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein dnak | protein | 603 | 41% helix, 28% strand | P0A6Y8 |
| B | Chaperone protein dnaj | protein | 63 | 75% helix, 0% strand | P08622 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.79 | 0.84 | 67 | ATP, MG |
| 2 | 364 | 0.61 | 0.77 | 37 | empty |
| 3 | 258 | 0.59 | 0.79 | 42 | empty |
| 4 | 250 | 0.51 | 0.75 | 28 | empty |
| 5 | 103 | 0.44 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5NRO · Structure of full-length DnaK with bound J-domain · 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 A against A, TM-score 0.99
- P08622 · AlphaFold monomer V2.0 prediction for chaperone protein dnaj (P08622) · a predicted model of the same protein · chain B against A, TM-score 0.90
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
- Every structure of UniProt P08622
- Elsewhere: RCSB PDB 5NRO · PDBe 5NRO · UniProt P0A6Y8 · UniProt P08622
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