MolNFT v1 · #86539 · protein
Open conformation of ATP-bound HSP70 homolog dnak
4B9Q · Chaperone protein dnak: “Open conformation of ATP-bound HSP70 homolog dnak”. X-ray diffraction, 2 ligands (ATP, MG), 20 pockets (best druggability 0.84). MolNFT v1 #86539 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4B9Q
- Type
- protein
- Length
- 2,388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak
- UniProt
- P0A6Y8
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.84
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, 28% strand | P0A6Y8 |
| B | Chaperone protein dnak | protein | 597 | 40% helix, 29% strand | P0A6Y8 |
| C | Chaperone protein dnak | protein | 595 | 41% helix, 29% strand | P0A6Y8 |
| D | Chaperone protein dnak | protein | 595 | 41% helix, 29% strand | P0A6Y8 |
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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.84 | 0.86 | 92 | ATP, MG |
| 2 | 900 | 0.82 | 0.84 | 73 | empty |
| 3 | 550 | 0.80 | 0.87 | 69 | ATP, MG |
| 4 | 721 | 0.77 | 0.81 | 62 | empty |
| 5 | 669 | 0.75 | 0.81 | 59 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1802 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1783 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 226 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified, 4 disulfide (engineered, disulfide).
Compared structures
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
- Elsewhere: RCSB PDB 4B9Q · PDBe 4B9Q · UniProt P0A6Y8
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