Research workbench
Crystal structure of the nucleotide exchange factor grpe bound to the ATPase domain of the molecular chaperone dnak
Analyse Crystal structure of the nucleotide exchange factor grpe bound to the ATPase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DKG
- Type
- protein
- Length
- 685 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotide exchange factor grpe; Molecular chaperone dnak
- UniProt
- P09372, P04475
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleotide exchange factor grpe | protein | 158 | 53% helix, 22% strand | P09372 |
| B | Nucleotide exchange factor grpe | protein | 151 | 56% helix, 22% strand | P09372 |
| D | Molecular chaperone dnak | protein | 376 | 39% helix, 28% strand | P04475 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.75 | 0.81 | 65 | empty |
| 2 | 338 | 0.74 | 0.86 | 56 | empty |
| 3 | 484 | 0.62 | 0.75 | 50 | empty |
| 4 | 88 | 0.35 | 0.74 | 17 | empty |
| 5 | 68 | 0.33 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2312 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1019 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1DKG · Crystal structure of the nucleotide exchange factor grpe bound to the ATPase domain of… · the same entry in another collection · chain A against A, TM-score 1.00
- P09372 · AlphaFold monomer V2.0 prediction for protein grpe (P09372) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P09372
- Every structure of UniProt P04475
- Elsewhere: RCSB PDB 1DKG · PDBe 1DKG · UniProt P09372 · UniProt P04475
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