Research workbench
Aaa ATPase domain of the proteasome- activating nucleotidase
Analyse Aaa ATPase domain of the proteasome- activating nucleotidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H4M
- Type
- protein
- Length
- 783 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome-activating nucleotidase
- UniProt
- Q58576
- Ligands
- ADP
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Proteasome-activating nucleotidase | protein | 261 | 52% helix, 14% strand | Q58576 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.65 | 0.77 | 41 | empty |
| 2 | 257 | 0.52 | 0.75 | 36 | empty |
| 3 | 218 | 0.48 | 0.75 | 32 | empty |
| 4 | 56 | 0.46 | 0.84 | 14 | empty |
| 5 | 109 | 0.41 | 0.76 | 33 | ADP |
Interfaces
3 interfaces between chains.
- A–C · 550 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 271 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3H4M · AAA ATPase domain of the proteasome- activating nucleotidase · the same entry in another collection · chain A against A, TM-score 1.00
- Q58576 · AlphaFold monomer V2.0 prediction for proteasome-activating nucleotidase (Q58576) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q58576
- Elsewhere: RCSB PDB 3H4M · PDBe 3H4M · UniProt Q58576
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