Research workbench
A dimeric ubiquitin formed by a single amino acid substitution
Analyse A dimeric ubiquitin formed by a single amino acid substitution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QK9
- Type
- protein
- Length
- 886 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-B
- UniProt
- P0CG47
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, L | Polyubiquitin-B | protein | 74 | 24% helix, 43% strand | P0CG47 |
| D | Polyubiquitin-B | protein | 73 | 25% helix, 42% strand | P0CG47 |
| E, H, J, K | Polyubiquitin-B | protein | 75 | 24% helix, 43% strand | P0CG47 |
| F | Polyubiquitin-B | protein | 72 | 25% helix, 42% strand | P0CG47 |
| G | Polyubiquitin-B | protein | 72 | 21% helix, 42% strand | P0CG47 |
| I | Polyubiquitin-B | protein | 73 | 21% helix, 41% strand | P0CG47 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.67 | 0.76 | 54 | empty |
| 2 | 537 | 0.62 | 0.75 | 64 | empty |
| 3 | 179 | 0.49 | 0.77 | 23 | empty |
| 4 | 87 | 0.37 | 0.76 | 23 | empty |
| 5 | 62 | 0.28 | 0.73 | 13 | empty |
Interfaces
18 interfaces between chains.
- K–L · 1906 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1898 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1838 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 1823 Ų buried · 38 hydrogen bonds · protein-protein
- I–J · 1784 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 6QK9 · A dimeric ubiquitin formed by a single amino acid substitution · 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 P0CG47
- Elsewhere: RCSB PDB 6QK9 · PDBe 6QK9 · UniProt P0CG47
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