Research workbench
Crystal structure of zebrafish TRAP1 with amppnp and mitoq
Analyse Crystal structure of zebrafish TRAP1 with amppnp and mitoq in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EXP
- Type
- protein
- Length
- 1,173 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TNF receptor-associated protein 1
- UniProt
- A8WFV1
- Ligands
- ANP, 05M, CO, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TNF receptor-associated protein 1 | protein | 574 | 40% helix, 22% strand | A8WFV1 |
| B | TNF receptor-associated protein 1 | protein | 599 | 41% helix, 21% strand | A8WFV1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- 05M · 2,3-dimethoxy-5-methyl-6-[10-(triphenyl-$l^{5}-phosphanyl)decyl]cyclohexa-2,5-diene-1,4-dione · ligand · 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 | 297 | 0.79 | 0.90 | 45 | ANP, MG |
| 2 | 323 | 0.77 | 0.89 | 44 | ANP, MG |
| 3 | 94 | 0.68 | 0.93 | 28 | empty |
| 4 | 462 | 0.65 | 0.78 | 40 | empty |
| 5 | 232 | 0.56 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 5247 Ų buried · 65 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7EXP · Crystal structure of zebrafish TRAP1 with AMPPNP and MitoQ · 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 7EXP · PDBe 7EXP · UniProt A8WFV1
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