MolNFT v1 · #90972 · protein
Crystal structure of the substrate binding domain of E.COLI dnak in complex with pr-39 (residues 1 to 15)
4EZO · Chaperone protein dnak: “Crystal structure of the substrate binding domain of E.COLI dnak in complex with pr-39 (residues 1 to 15)”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.75). MolNFT v1 #90972 on…
- PDB
- 4EZO
- Type
- protein
- Length
- 442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak; Antibacterial protein pr-39
- UniProt
- P0A6Y8, P80054
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein dnak | protein | 211 | 38% helix, 28% strand | P0A6Y8 |
| B | Chaperone protein dnak | protein | 215 | 41% helix, 28% strand | P0A6Y8 |
| C | Antibacterial protein pr-39 | protein | 8 | 0% helix, 13% strand | P80054 |
| D | Antibacterial protein pr-39 | protein | 8 | 0% helix, 25% strand | P80054 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.75 | 0.85 | 43 | SO4 |
| 2 | 371 | 0.74 | 0.85 | 40 | SO4 |
| 3 | 102 | 0.52 | 0.83 | 20 | empty |
| 4 | 75 | 0.48 | 0.83 | 19 | empty |
| 5 | 80 | 0.37 | 0.77 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–C · 641 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 613 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 489 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 118 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4EZO · Crystal structure of the substrate binding domain of E.coli DnaK in complex with PR-39… · the same entry in another collection · chain D against D, TM-score 1.00
- P80054 · AlphaFold monomer V2.0 prediction for antibacterial protein pr-39 (P80054) · a predicted model of the same protein · chain C against A, TM-score 0.52
- 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
- Every structure of UniProt P80054
- Elsewhere: RCSB PDB 4EZO · PDBe 4EZO · UniProt P0A6Y8 · UniProt P80054
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