Research workbench
Ubiquitin variant (UBV.FL10.1) bound to a human SKP1-FBL10 fragment complex.
Analyse Ubiquitin variant (UBV.FL10.1) bound to a human SKP1-FBL10 fragment complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BVA
- Type
- protein
- Length
- 549 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-phase kinase-associated protein 1; Lysine-specific demethylase 2B; Polyubiquitin-B
- EC
- 1.14.11.27
- UniProt
- P63208, Q8NHM5, P0CG47
- Pockets
- 9 · best druggability 0.49
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | S-phase kinase-associated protein 1 | protein | 150 | 47% helix, 8% strand | P63208 |
| E, F | Lysine-specific demethylase 2B (EC 1.14.11.27) | protein | 40 | 53% helix, 0% strand | Q8NHM5 |
| B | Polyubiquitin-B | protein | 81 | 22% helix, 37% strand | P0CG47 |
| A | Polyubiquitin-B | protein | 86 | 21% helix, 35% strand | P0CG47 |
| C | S-phase kinase-associated protein 1 | protein | 152 | 49% helix, 8% strand | P63208 |
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.49 | 0.76 | 22 | empty |
| 2 | 55 | 0.47 | 0.84 | 12 | empty |
| 3 | 189 | 0.46 | 0.75 | 22 | empty |
| 4 | 117 | 0.39 | 0.75 | 23 | empty |
| 5 | 96 | 0.38 | 0.76 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–F · 1070 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 931 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 903 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 806 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 175 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BVA · Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. · the same entry in another collection · chain B against B, 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 C against A, TM-score 0.92
- Q8NHM5 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 2B (Q8NHM5) · a predicted model of the same protein · chain E against A, TM-score 0.82
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 Q8NHM5
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6BVA · PDBe 6BVA · UniProt P63208 · UniProt Q8NHM5 · UniProt P0CG47
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