Research workbench
Ubiquitin binding variants
Analyse Ubiquitin binding variants in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NXL
- Type
- protein
- Length
- 592 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.803
- Source
- Homo sapiens
- Molecule
- Polyubiquitin-B
- UniProt
- B4DV12
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.803 · 4 distinct chains · 24% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Polyubiquitin-B | protein | 75 | 24% helix, 45% strand | B4DV12 |
| B, D, F | Polyubiquitin-B | protein | 74 | 24% helix, 43% strand | B4DV12 |
| C, G | Polyubiquitin-B | protein | 73 | 25% helix, 42% strand | B4DV12 |
| H | Polyubiquitin-B | protein | 74 | 24% helix, 43% strand | B4DV12 |
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 | 442 | 0.74 | 0.83 | 60 | empty |
| 2 | 233 | 0.66 | 0.83 | 40 | empty |
| 3 | 51 | 0.37 | 0.81 | 16 | empty |
| 4 | 52 | 0.37 | 0.80 | 16 | empty |
| 5 | 50 | 0.32 | 0.78 | 15 | empty |
Interfaces
20 interfaces between chains.
- G–H · 1722 Ų buried · 42 hydrogen bonds · protein-protein
- A–E · 1702 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1701 Ų buried · 40 hydrogen bonds · protein-protein
- B–F · 1695 Ų buried · 41 hydrogen bonds · protein-protein
- D–F · 696 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6NXL · Ubiquitin binding variants · 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 B4DV12
- Elsewhere: RCSB PDB 6NXL · PDBe 6NXL · UniProt B4DV12
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