Research workbench
Crystal structure of the substrate binding domain of E.COLI dnak in complex with pr-bombesin in space group P21212
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
- 4EZV
- Type
- protein
- Length
- 457 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak; Proline rich bombesin-related protein
- UniProt
- P0A6Y8, Q8QFP2
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein dnak | protein | 219 | 42% helix, 27% strand | P0A6Y8 |
| B | Chaperone protein dnak | protein | 216 | 42% helix, 27% strand | P0A6Y8 |
| C | Proline rich bombesin-related protein | protein | 12 | 0% helix, 25% strand | Q8QFP2 |
| D | Proline rich bombesin-related protein | protein | 10 | 0% helix, 30% strand | Q8QFP2 |
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.76 | 0.79 | 64 | empty |
| 2 | 353 | 0.76 | 0.86 | 36 | empty |
| 3 | 63 | 0.72 | 0.98 | 17 | empty |
| 4 | 54 | 0.72 | 0.98 | 16 | empty |
| 5 | 141 | 0.56 | 0.82 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1485 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 695 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 691 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 181 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 173 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4EZV · Crystal structure of the substrate binding domain of E.coli DnaK in complex with… · 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 0.49
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 Q8QFP2
- Elsewhere: RCSB PDB 4EZV · PDBe 4EZV · UniProt P0A6Y8 · UniProt Q8QFP2
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