6C16: Ubiquitin variant
Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Determined by X-ray diffraction at 3.27 Å resolution. Released 18 Jul 2018.
- Method
- X-ray diffraction
- Resolution
- 3.27 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 3,529
- Mol. weight
- 69.47 kDa
- Released
- 18 Jul 2018
Explore 6C16 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6C16 contains 30 α-helices and 26 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 9 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 1 |
| β-strand | 13-16 | 4 | 1 |
| α-helix | 18-21 | 4 | |
| α-helix | 25-30 | 6 | |
| α-helix | 44 | 1 | |
| β-strand | 45-46 | 2 | 1 |
| α-helix | 52-64 | 13 | |
| α-helix | 87-92 | 6 | |
| α-helix | 97-109 | 13 | |
| α-helix | 113-127 | 15 | |
| α-helix | 132-139 | 8 | |
| α-helix | 147-154 | 8 | |
Chain B: 9 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 2 |
| β-strand | 13-17 | 5 | 2 |
| α-helix | 18-21 | 4 | |
| α-helix | 25-30 | 6 | |
| α-helix | 44 | 1 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 52-64 | 13 | |
| α-helix | 87-92 | 6 | |
| α-helix | 97-109 | 13 | |
| α-helix | 113-127 | 15 | |
| α-helix | 132-139 | 8 | |
| α-helix | 147-156 | 10 | |
Chain C: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 894-904 | 11 | |
| α-helix | 907-913 | 7 | |
| α-helix | 918-924 | 7 | |
Chain D: 3 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 3 |
| β-strand | 10 | 1 | 4 |
| β-strand | 11d | 1 | 4 |
| β-strand | 12-16 | 5 | 3 |
| β-strand | 22 | 1 | 5 |
| α-helix | 23-31 | 9 | |
| β-strand | 41-45 | 5 | 6 |
| β-strand | 48-49 | 2 | 6 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 5 |
| α-helix | 58-60 | 3 | |
| β-strand | 66 | 1 | 3 |
| β-strand | 68-71 | 4 | 6 |
Chain F: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 894-902 | 9 | |
| α-helix | 907-913 | 7 | |
| α-helix | 918-924 | 7 | |
Chain H: 3 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1-6 | 6 | 7 |
| β-strand | 10 | 1 | 8 |
| β-strand | 11d | 1 | 8 |
| β-strand | 12-17 | 6 | 7 |
| β-strand | 22 | 1 | 9 |
| α-helix | 23-33 | 11 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-44 | 4 | 10 |
| β-strand | 49 | 1 | 10 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 9 |
| β-strand | 66 | 1 | 7 |
| β-strand | 68-71 | 4 | 10 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| S-phase kinase-associated protein 1 | A, B | protein | 165 | Homo sapiens | P63208 (AlphaFold model) |
| Lysine-specific demethylase 2A | C, F | protein | 47 | Homo sapiens | Q9Y2K7 (AlphaFold model) |
| Polyubiquitin-B | D, H | protein | 86 | Homo sapiens | P0CG47 (AlphaFold model) |
Sequence of entity 1 (A, B), FASTA
>6C16_1 S-phase kinase-associated protein 1 (chains A, B)
GAMPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKV
IQWCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDV
TCKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 2 (C, F), FASTA
>6C16_2 Lysine-specific demethylase 2A (chains C, F)
GAGDESWMQREVWMSVFRYLSRRELCECMRVCKTWYKWCCDKRLWTK
Sequence of entity 3 (D, H), FASTA
>6C16_3 Polyubiquitin-B (chains D, H)
GSGMQIFVKTFRDRLRNLLPQTITLEVEPSDTIENVKAKIQDKEGIPPDQQVLIFSRKRL
EDGRTLSDYNIQKESTLRLVLVFGRR
Primary citation
A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases. Gorelik, M., Manczyk, N., Pavlenco, A. et al. Structure (2018) 26:1226. DOI 10.1016/j.str.2018.06.004 · PubMed
Other PDB entries of the same protein (UniProt P63208 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1FS1 1.8 Å, Insights into scf ubiquitin ligases from the structure of the SKP1-SKP2 complex
- 6M90 2.05 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex
- 2AST 2.3 Å, Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide
- 6M92 2.35 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex
- 2E31 2.4 Å, Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase
- 6M91 2.4 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex
- 2OVR 2.5 Å, Structure of the Skp1-Fbw7-CyclinEdegN complex
- 6M93 2.5 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex
- 6WNX 2.5 Å, FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide
- 5IBK 2.5 Å, Skp1-F-box in complex with a ubiquitin variant
- 6O60 2.5 Å, Crystal structure of GGTase3-FBXL2-SKP1 complex
- 5JH5 2.55 Å, Structural Basis for the Hierarchical Assembly of the Core of PRC1.1
Browse structure collections
About this viewer
MolViewer shows 6C16 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.