Research workbench
Heterodimeric SPYCATCHER/SPYTAG-fused zebrafish TRAP1 in ATP/ADP- hybrid state
Analyse Heterodimeric SPYCATCHER/SPYTAG-fused zebrafish TRAP1 in ATP/ADP- hybrid state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TTH
- Type
- protein
- Length
- 1,292 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-terminal spycatcher fusion of wildtype zebrafish TNF receptor-associated protein 1…
- UniProt
- A8WFV1, Q8G9G1
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-terminal spycatcher fusion of wildtype zebrafish TNF receptor-associated protein 1 | protein | 671 | 37% helix, 25% strand | A8WFV1, Q8G9G1 |
| B | C-terminal spytag fusion of R417A zebrafish TNF receptor- associated protein 1 | protein | 621 | 40% helix, 21% strand | A8WFV1, Q8G9G1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- BEF · Beryllium trifluoride ion · ligand · 2 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.79 | 0.85 | 68 | ADP, BEF, MG |
| 2 | 269 | 0.78 | 0.91 | 42 | ADP, BEF, MG |
| 3 | 967 | 0.71 | 0.75 | 81 | empty |
| 4 | 101 | 0.68 | 0.92 | 31 | empty |
| 5 | 368 | 0.67 | 0.80 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 6408 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 5TTH · Heterodimeric SpyCatcher/SpyTag-fused zebrafish TRAP1 in ATP/ADP-hybrid state · 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
- Every structure of UniProt Q8G9G1
- Elsewhere: RCSB PDB 5TTH · PDBe 5TTH · UniProt A8WFV1 · UniProt Q8G9G1
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