MolNFT v1 · #95766 · protein
Structure of mitochondrial HSP90 (TRAP1) with ADP-BEF3
4J0B · TNF receptor-associated protein 1: “Structure of mitochondrial HSP90 (TRAP1) with ADP-BEF3”. X-ray diffraction, 4 ligands (ADP, BEF, CO), 20 pockets (best druggability 0.78). MolNFT v1 #95766 on GenesisL1: 3D structure, binding…
- PDB
- 4J0B
- Type
- protein
- Length
- 1,203 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TNF receptor-associated protein 1
- UniProt
- A8WFV1
- Ligands
- ADP, BEF, CO, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TNF receptor-associated protein 1 | protein | 594 | 38% helix, 21% strand | A8WFV1 |
| B | TNF receptor-associated protein 1 | protein | 609 | 41% helix, 21% strand | A8WFV1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- BEF · Beryllium trifluoride ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.78 | 0.89 | 43 | ADP, BEF, MG |
| 2 | 297 | 0.77 | 0.89 | 44 | ADP, BEF, MG |
| 3 | 475 | 0.73 | 0.83 | 60 | empty |
| 4 | 530 | 0.73 | 0.82 | 68 | empty |
| 5 | 130 | 0.63 | 0.87 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 5603 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4J0B · Structure of mitochondrial Hsp90 (TRAP1) with ADP-BeF3 · 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 4J0B · PDBe 4J0B · UniProt A8WFV1
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