MolNFT v1 · #144684 · protein
Ubiquitin variant (UBV.FBL10.1) bound to a human SKP1-FBL11 fragment complex.
6C16 · S-phase kinase-associated protein 1: “Ubiquitin variant (UBV.FBL10.1) bound to a human SKP1-FBL11 fragment complex.”. X-ray diffraction, 5 pockets (best druggability 0.70). MolNFT v1 #144684 on GenesisL1: 3D structure, binding sites…
- PDB
- 6C16
- Type
- protein
- Length
- 510 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 2A; Polyubiquitin-B
- EC
- 1.14.11.27
- UniProt
- P63208, Q9Y2K7, P0CG47
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-phase kinase-associated protein 1 | protein | 134 | 54% helix, 7% strand | P63208 |
| B | S-phase kinase-associated protein 1 | protein | 139 | 54% helix, 9% strand | P63208 |
| C | Lysine-specific demethylase 2A (EC 1.14.11.27) | protein | 35 | 71% helix, 0% strand | Q9Y2K7 |
| D | Polyubiquitin-B | protein | 80 | 15% helix, 33% strand | P0CG47 |
| F | Lysine-specific demethylase 2A (EC 1.14.11.27) | protein | 40 | 58% helix, 0% strand | Q9Y2K7 |
| H | Polyubiquitin-B | protein | 82 | 17% helix, 32% strand | P0CG47 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.70 | 0.82 | 52 | empty |
| 2 | 50 | 0.69 | 0.97 | 19 | empty |
| 3 | 120 | 0.65 | 0.88 | 23 | empty |
| 4 | 308 | 0.54 | 0.74 | 41 | empty |
| 5 | 124 | 0.47 | 0.78 | 21 | empty |
Interfaces
7 interfaces between chains.
- B–F · 771 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 717 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 706 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 683 Ų buried · 10 hydrogen bonds · protein-protein
- C–H · 176 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6C16 · Ubiquitin variant (UbV.Fbl10.1) 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 B against A, TM-score 0.94
- Q9Y2K7 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 2A (Q9Y2K7) · a predicted model of the same protein · chain F 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 Q9Y2K7
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6C16 · PDBe 6C16 · UniProt P63208 · UniProt Q9Y2K7 · UniProt P0CG47
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