Research workbench
Crystal structure of mitochondrial Hsp90 (TRAP1) with AMPPNP
Analyse Crystal structure of mitochondrial Hsp90 (TRAP1) with AMPPNP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IPE
- Type
- protein
- Length
- 1,189 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.289
- Source
- Danio rerio
- Molecule
- TNF receptor-associated protein 1
- UniProt
- A8WFV1
- Ligands
- ANP, CO, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.289 · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TNF receptor-associated protein 1 | protein | 588 | 43% helix, 21% strand | A8WFV1 |
| B | TNF receptor-associated protein 1 | protein | 601 | 41% helix, 21% strand | A8WFV1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.80 | 0.92 | 43 | ANP, MG |
| 2 | 302 | 0.78 | 0.89 | 42 | ANP, MG |
| 3 | 95 | 0.69 | 0.92 | 29 | empty |
| 4 | 631 | 0.66 | 0.75 | 53 | empty |
| 5 | 562 | 0.64 | 0.76 | 64 | empty |
Interfaces
1 interface between chains.
- A–B · 5393 Ų buried · 66 hydrogen bonds · protein-protein
Compared structures
- 4IPE · Crystal structure of mitochondrial HSP90 (TRAP1) with amppnp · 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 A8WFV1
- Elsewhere: RCSB PDB 4IPE · PDBe 4IPE · UniProt A8WFV1
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