MolNFT v1 · #180190 · protein
Restraining state of a truncated HSP70 dnak
7KRT · Chaperone protein dnak: “Restraining state of a truncated HSP70 dnak”. X-ray diffraction, 2 ligands (ATP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #180190 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KRT
- Type
- protein
- Length
- 2,396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak
- UniProt
- A0A6D2W465
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Chaperone protein dnak | protein | 599 | 41% helix, 28% strand | A0A6D2W465 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.86 | 0.88 | 105 | MG, ATP |
| 2 | 474 | 0.81 | 0.89 | 61 | MG, ATP |
| 3 | 373 | 0.80 | 0.89 | 55 | MG, ATP |
| 4 | 941 | 0.76 | 0.79 | 73 | empty |
| 5 | 273 | 0.72 | 0.86 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1625 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1472 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 338 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 213 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 211 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7KRT · Restraining state of a truncated Hsp70 DnaK · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A6D2W465
- Elsewhere: RCSB PDB 7KRT · PDBe 7KRT · UniProt A0A6D2W465
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