Research workbench
Ubiquitin variant (UBV.FL11.1) bound to a human SKP1-FBL11 fragment complex.
Analyse Ubiquitin variant (UBV.FL11.1) bound to a human SKP1-FBL11 fragment complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BYH
- Type
- protein
- Length
- 803 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-phase kinase-associated protein 1; Lysine-specific demethylase 2A; Polyubiquitin-B
- EC
- 1.14.11.27
- UniProt
- P63208, Q9Y2K7, P0CG47
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-phase kinase-associated protein 1 | protein | 145 | 51% helix, 8% strand | P63208 |
| B | S-phase kinase-associated protein 1 | protein | 150 | 55% helix, 9% strand | P63208 |
| E, F | Lysine-specific demethylase 2A (EC 1.14.11.27) | protein | 45 | 53% helix, 0% strand | Q9Y2K7 |
| G | S-phase kinase-associated protein 1 | protein | 126 | 52% helix, 10% strand | P63208 |
| I | Lysine-specific demethylase 2A (EC 1.14.11.27) | protein | 39 | 62% helix, 0% strand | Q9Y2K7 |
| C | Polyubiquitin-B | protein | 84 | 21% helix, 39% strand | P0CG47 |
| D | Polyubiquitin-B | protein | 85 | 21% helix, 39% strand | P0CG47 |
| H | Polyubiquitin-B | protein | 84 | 18% helix, 39% strand | P0CG47 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.60 | 0.75 | 56 | empty |
| 2 | 228 | 0.56 | 0.78 | 23 | empty |
| 3 | 135 | 0.54 | 0.81 | 25 | empty |
| 4 | 219 | 0.53 | 0.77 | 22 | empty |
| 5 | 180 | 0.50 | 0.77 | 23 | empty |
Interfaces
11 interfaces between chains.
- B–F · 1390 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1189 Ų buried · 12 hydrogen bonds · protein-protein
- G–I · 717 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 662 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 621 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6BYH · Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. · the same entry in another collection · chain H against H, TM-score 1.00
- P63208 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 1 (P63208) · a predicted model of the same protein · chain G against A, TM-score 0.97
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 P63208
- Every structure of UniProt Q9Y2K7
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6BYH · PDBe 6BYH · UniProt P63208 · UniProt Q9Y2K7 · UniProt P0CG47
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