MolNFT v1 · #159460 · protein
Crystal structure of branched K11/K48-linked tri-ubiquitin
6OQ1: “Crystal structure of branched K11/K48-linked tri-ubiquitin”. X-ray diffraction, 5 pockets (best druggability 0.79). MolNFT v1 #159460 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OQ1
- Type
- protein
- Length
- 446 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- UniProt
- P0CG47
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin | protein | 76 | 24% helix, 34% strand | P0CG47 |
| C, D | Ubiquitin | protein | 76 | 24% helix, 33% strand | P0CG47 |
| E, F | Ubiquitin | protein | 71 | 25% helix, 32% 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 | 1041 | 0.79 | 0.80 | 86 | empty |
| 2 | 363 | 0.61 | 0.77 | 36 | empty |
| 3 | 97 | 0.40 | 0.77 | 17 | empty |
| 4 | 93 | 0.38 | 0.76 | 18 | empty |
| 5 | 108 | 0.36 | 0.74 | 18 | empty |
Interfaces
10 interfaces between chains.
- A–F · 712 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 689 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 562 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 359 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 296 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide (isopeptide).
Compared structures
- 6OQ1 · Crystal Structure of Branched K11/K48-Linked Tri-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 P0CG47
- Elsewhere: RCSB PDB 6OQ1 · PDBe 6OQ1 · UniProt P0CG47
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