MolNFT v1 · #121976 · protein
SKP1-F-box in complex with a ubiquitin variant
5IBK · S-phase kinase-associated protein 1,S-phase kinase…: “SKP1-F-box in complex with a ubiquitin variant”. X-ray diffraction, 5 pockets (best druggability 0.81). MolNFT v1 #121976 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5IBK
- Type
- protein
- Length
- 526 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-phase kinase-associated protein 1,S-phase kinase- associated protein 1; F-BOX/WD…
- UniProt
- P63208, Q969H0, P0CG47
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-phase kinase-associated protein 1,S-phase kinase- associated protein 1 | protein | 141 | 53% helix, 10% strand | P63208 |
| B | F-BOX/WD repeat-containing protein 7 | protein | 46 | 65% helix, 0% strand | Q969H0 |
| F | Polyubiquitin-B | protein | 75 | 24% helix, 36% strand | P0CG47 |
| C | Polyubiquitin-B | protein | 76 | 24% helix, 36% strand | P0CG47 |
| D | S-phase kinase-associated protein 1,S-phase kinase- associated protein 1 | protein | 140 | 57% helix, 10% strand | P63208 |
| E | F-BOX/WD repeat-containing protein 7 | protein | 48 | 63% helix, 0% strand | Q969H0 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.81 | 0.83 | 62 | empty |
| 2 | 101 | 0.45 | 0.79 | 22 | empty |
| 3 | 74 | 0.36 | 0.76 | 13 | empty |
| 4 | 100 | 0.33 | 0.73 | 19 | empty |
| 5 | 63 | 0.29 | 0.74 | 14 | empty |
Interfaces
12 interfaces between chains.
- D–E · 1504 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1391 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 748 Ų buried · 12 hydrogen bonds · protein-protein
- F–D · 737 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 483 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5IBK · Skp1-F-box in complex with a ubiquitin variant · the same entry in another collection · chain E against E, 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 A against A, TM-score 0.93
- Q969H0 · AlphaFold monomer V2.0 prediction for F-BOX/WD repeat-containing protein 7 (Q969H0) · a predicted model of the same protein · chain B against A, TM-score 0.84
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 Q969H0
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5IBK · PDBe 5IBK · UniProt P63208 · UniProt Q969H0 · UniProt P0CG47
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