6BYH: Ubiquitin Variant
Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Determined by X-ray diffraction at 2.61 Å resolution. Released 18 Jul 2018.
- Method
- X-ray diffraction
- Resolution
- 2.61 Å
- Organism
- Homo sapiens
- Chains
- 9
- Atoms
- 6,235
- Mol. weight
- 104.24 kDa
- Released
- 18 Jul 2018
Explore 6BYH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6BYH contains 48 α-helices and 30 β-strands across 9 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: 10 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 1 |
| β-strand | 13-17 | 5 | 1 |
| α-helix | 18-21 | 4 | |
| α-helix | 25-32 | 8 | |
| α-helix | 44 | 1 | |
| β-strand | 45-46 | 2 | 1 |
| α-helix | 52-64 | 13 | |
| α-helix | 65-67 | 3 | |
| α-helix | 87-92 | 6 | |
| α-helix | 97-110 | 14 | |
| α-helix | 113-124 | 12 | |
| α-helix | 132-139 | 8 | |
| α-helix | 147-152 | 6 | |
Chain B: 10 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 2 |
| β-strand | 13-17 | 5 | 2 |
| α-helix | 18-21 | 4 | |
| α-helix | 25-32 | 8 | |
| α-helix | 43-44 | 2 | |
| β-strand | 45-47 | 3 | 2 |
| α-helix | 52-64 | 13 | |
| α-helix | 65-67 | 3 | |
| α-helix | 87-92 | 6 | |
| α-helix | 97-110 | 14 | |
| α-helix | 113-125 | 13 | |
| α-helix | 132-139 | 8 | |
| α-helix | 147-159 | 13 | |
Chains C and D: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1-9 | 9 | 4 |
| β-strand | 11f-17 | 9 | 4 |
| β-strand | 22 | 1 | 5 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 4 |
| β-strand | 48-49 | 2 | 4 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 5 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 4 |
Chains E, F and I: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 892-902 | 11 | |
| α-helix | 907-913 | 7 | |
| α-helix | 918-923 | 6 | |
Chain G: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 3 |
| β-strand | 13-17 | 5 | 3 |
| α-helix | 18-21 | 4 | |
| α-helix | 25-32 | 8 | |
| α-helix | 43-44 | 2 | |
| β-strand | 45-46 | 2 | 3 |
| α-helix | 52-64 | 13 | |
| α-helix | 87-92 | 6 | |
| α-helix | 97-110 | 14 | |
| α-helix | 113-124 | 12 | |
| α-helix | 132-139 | 8 | |
Chain H: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1-9 | 9 | 8 |
| β-strand | 11f-17 | 9 | 8 |
| β-strand | 22 | 1 | 9 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 8 |
| β-strand | 48-49 | 2 | 8 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 9 |
| β-strand | 66-71 | 6 | 8 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| S-phase kinase-associated protein 1 | A, B, G | protein | 165 | Homo sapiens | P63208 (AlphaFold model) |
| Lysine-specific demethylase 2A | E, F, I | protein | 47 | Homo sapiens | Q9Y2K7 (AlphaFold model) |
| Polyubiquitin-B | C, D, H | protein | 87 | Homo sapiens | P0CG47 (AlphaFold model) |
Sequence of entity 1 (A, B, G), FASTA
>6BYH_1 S-phase kinase-associated protein 1 (chains A, B, G)
GAMPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKV
IQWCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDV
TCKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 2 (E, F, I), FASTA
>6BYH_2 Lysine-specific demethylase 2A (chains E, F, I)
GAGDESWMQREVWMSVFRYLSRRELCECMRVCKTWYKWCCDKRLWTK
Sequence of entity 3 (C, D, H), FASTA
>6BYH_3 Polyubiquitin-B (chains C, D, H)
GSGMQIFVKTRHSYKHGLIENSTITLEVEPSDTIENVKAKIQDKEGIPPDQQVLIFSRKR
LEDGRTLSDYNIQKESTLRLVLVFGRR
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
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