Research workbench
Structure of K11-linked di-ubiquitin
Analyse Structure of K11-linked di-ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NOB
- Type
- protein
- Length
- 604 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- UniProt
- P62988
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 77 | 23% helix, 36% strand | P62988 |
| B | Ubiquitin | protein | 74 | 20% helix, 34% strand | P62988 |
| C, D, E | Ubiquitin | protein | 75 | 20% helix, 36% strand | P62988 |
| F | Ubiquitin | protein | 76 | 20% helix, 34% strand | P62988 |
| G | Ubiquitin | protein | 75 | 20% helix, 33% strand | P62988 |
| H | Ubiquitin | protein | 77 | 19% helix, 35% strand | P62988 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, E, F, C, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.70 | 0.82 | 50 | empty |
| 2 | 323 | 0.65 | 0.80 | 49 | SO4 |
| 3 | 179 | 0.59 | 0.82 | 22 | empty |
| 4 | 125 | 0.51 | 0.80 | 24 | SO4 |
| 5 | 100 | 0.43 | 0.78 | 20 | empty |
Interfaces
14 interfaces between chains.
- G–H · 898 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 880 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 803 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 353 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 3NOB · Structure of K11-linked di-ubiquitin · 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 P62988
- Elsewhere: RCSB PDB 3NOB · PDBe 3NOB · UniProt P62988
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