Research workbench
Crystal structure of the dnak C-terminus with the substrate peptide nrllltg
Analyse Crystal structure of the dnak C-terminus with the substrate peptide nrllltg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R5I
- Type
- protein
- Length
- 228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak; HSP70/DNAK substrate peptide: nrllltg
- UniProt
- P0A6Y8
- Ligands
- PO4, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein dnak | protein | 222 | 41% helix, 26% strand | P0A6Y8 |
| B | HSP70/DNAK substrate peptide: nrllltg | protein | 6 | 0% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.63 | 0.82 | 25 | empty |
| 2 | 71 | 0.35 | 0.77 | 19 | PO4 |
Interfaces
1 interface between chains.
- A–B · 600 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4R5I · Crystal structure of the DnaK C-terminus with the substrate peptide NRLLLTG · 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 0.47
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 4R5I · PDBe 4R5I · UniProt P0A6Y8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.