Research workbench
Caldiarchaeum subterraneum UBIQUITIN:RPN11-homolog complex
Analyse Caldiarchaeum subterraneum UBIQUITIN:RPN11-homolog complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FNN
- Type
- protein
- Length
- 481 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome regulatory subunit N11-like protein; Ubiquitin-like protein
- EC
- 3.4.19.12
- UniProt
- E6N8B9, E6N8B8
- Ligands
- ZN, SO4
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome regulatory subunit N11-like protein (EC 3.4.19.12) | protein | 149 | 26% helix, 42% strand | E6N8B9 |
| B | 26S proteasome regulatory subunit N11-like protein (EC 3.4.19.12) | protein | 152 | 26% helix, 36% strand | E6N8B9 |
| C, D | Ubiquitin-like protein | protein | 90 | 21% helix, 31% strand | E6N8B8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.42 | 0.80 | 22 | empty |
| 2 | 65 | 0.41 | 0.80 | 18 | empty |
| 3 | 52 | 0.37 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1273 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1255 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1113 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6FNN · Caldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex · 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 E6N8B9
- Every structure of UniProt E6N8B8
- Elsewhere: RCSB PDB 6FNN · PDBe 6FNN · UniProt E6N8B9 · UniProt E6N8B8
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