MolNFT v1 · #180063 · protein
Restraining state of near full-length HSP70 dnak
7KO2 · Chaperone protein dnak: “Restraining state of near full-length HSP70 dnak”. X-ray diffraction, 3 ligands (ATP, MG, SO4), 20 pockets (best druggability 0.85). MolNFT v1 #180063 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7KO2
- Type
- protein
- Length
- 2,399 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak
- UniProt
- A0A6D2W465
- Ligands
- ATP, MG, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein dnak | protein | 601 | 41% helix, 30% strand | A0A6D2W465 |
| B | Chaperone protein dnak | protein | 603 | 41% helix, 28% strand | A0A6D2W465 |
| C | Chaperone protein dnak | protein | 595 | 41% helix, 29% strand | A0A6D2W465 |
| D | Chaperone protein dnak | protein | 600 | 41% helix, 29% 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
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.85 | 0.86 | 118 | MG, ATP |
| 2 | 675 | 0.79 | 0.84 | 64 | empty |
| 3 | 385 | 0.75 | 0.86 | 48 | MG, ATP |
| 4 | 214 | 0.75 | 0.90 | 34 | empty |
| 5 | 246 | 0.75 | 0.89 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1801 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1749 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 205 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7KO2 · Restraining state of near full-length 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 7KO2 · PDBe 7KO2 · UniProt A0A6D2W465
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