Research workbench
Zebrafish TRAP1 bound to amppnp and calcium in the asymmetric closed state
Analyse Zebrafish TRAP1 bound to amppnp and calcium in the asymmetric closed state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D14
- Type
- protein
- Length
- 1,185 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, CA
- Pockets
- 17 · best druggability 0.79
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 | 580 | 38% helix, 20% strand | A8WFV1 |
| B | TNF receptor-associated protein 1 | protein | 605 | 41% helix, 21% strand | A8WFV1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- CA · Calcium 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.79 | 0.91 | 50 | ANP, CA |
| 2 | 277 | 0.75 | 0.88 | 44 | ANP |
| 3 | 623 | 0.69 | 0.78 | 70 | empty |
| 4 | 430 | 0.67 | 0.79 | 48 | empty |
| 5 | 510 | 0.63 | 0.76 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 5752 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 6D14 · Zebrafish TRAP1 bound to AMPPNP and calcium in the asymmetric closed 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
- Elsewhere: RCSB PDB 6D14 · PDBe 6D14 · UniProt A8WFV1
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