Research workbench
Crystal structure of the substrate binding domain of E.COLI dnak in complex with the designer peptide nrliltg
Analyse Crystal structure of the substrate binding domain of E.COLI dnak in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EZY
- Type
- protein
- Length
- 224 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak; Synthetic peptide nrliltg
- UniProt
- P0A6Y8
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein dnak | protein | 219 | 42% helix, 26% strand | P0A6Y8 |
| B | Synthetic peptide nrliltg | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.55 | 0.82 | 22 | empty |
| 2 | 79 | 0.33 | 0.74 | 16 | empty |
| 3 | 57 | 0.26 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4EZY · Crystal structure of the substrate binding domain of E.coli DnaK in complex with the… · 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 0.46
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 4EZY · PDBe 4EZY · UniProt P0A6Y8
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