Research workbench
Full-length human mitochondrial HSP90 (TRAP1) with AMP-pnp
Analyse Full-length human mitochondrial HSP90 (TRAP1) with AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KCK
- Type
- protein
- Length
- 1,220 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock protein 75 kda, mitochondrial
- UniProt
- Q12931
- Ligands
- ANP, MG, K
- Pockets
- 17 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heat shock protein 75 kda, mitochondrial | protein | 607 | 39% helix, 20% strand | Q12931 |
| B | Heat shock protein 75 kda, mitochondrial | protein | 613 | 41% helix, 18% strand | Q12931 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.79 | 0.92 | 39 | MG, K, ANP |
| 2 | 248 | 0.77 | 0.90 | 39 | MG, K, ANP |
| 3 | 895 | 0.76 | 0.79 | 84 | empty |
| 4 | 55 | 0.70 | 0.97 | 19 | empty |
| 5 | 404 | 0.68 | 0.81 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 5523 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 7KCK · Full-length human mitochondrial Hsp90 (TRAP1) with AMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00
- Q12931 · AlphaFold monomer V2.0 prediction for heat shock protein 75 kda, mitochondrial (Q12931) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q12931
- Elsewhere: RCSB PDB 7KCK · PDBe 7KCK · UniProt Q12931
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