Research workbench
Crystal structure of the prokaryotic ubiquintin-like protein pup complexed with the hexameric proteasomal ATPase mpa which includes the amino terminal coiled coil domain and the inter domain
Analyse Crystal structure of the prokaryotic ubiquintin-like protein pup complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M9D
- Type
- protein
- Length
- 2,418 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome-associated ATPase; Prokaryotic ubiquitin-like protein pup
- UniProt
- P63345, O33246
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, J, K, L, M, N, O | Proteasome-associated ATPase | protein | 186 | 19% helix, 28% strand | P63345 |
| G, H, I, P, Q, R | Prokaryotic ubiquitin-like protein pup | protein | 31 | 29% helix, 0% strand | O33246 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.66 | 0.81 | 46 | empty |
| 2 | 233 | 0.66 | 0.84 | 33 | empty |
| 3 | 236 | 0.65 | 0.83 | 33 | empty |
| 4 | 248 | 0.65 | 0.83 | 33 | empty |
| 5 | 279 | 0.65 | 0.81 | 29 | empty |
Interfaces
27 interfaces between chains.
- N–O · 2083 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 2063 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 2059 Ų buried · 10 hydrogen bonds · protein-protein
- L–M · 2049 Ų buried · 9 hydrogen bonds · protein-protein
- J–K · 2043 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3M9D · Crystal structure of the prokaryotic ubiquintin-like protein Pup complexed with the… · 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 P63345
- Every structure of UniProt O33246
- Elsewhere: RCSB PDB 3M9D · PDBe 3M9D · UniProt P63345 · UniProt O33246
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