Research workbench
Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor in complex with human Nedd8
Analyse Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F8C
- Type
- protein
- Length
- 644 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Homo sapiens; Yersinia pseudotuberculosis
- Molecule
- Cycle Inhibiting Factor; NEDD8
- UniProt
- B1JJZ9, Q15843
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.95 · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cycle Inhibiting Factor | protein | 249 | 47% helix, 14% strand | B1JJZ9 |
| B | NEDD8 | protein | 74 | 26% helix, 32% strand | Q15843 |
| C | Cycle Inhibiting Factor | protein | 248 | 49% helix, 13% strand | B1JJZ9 |
| D | NEDD8 | protein | 73 | 25% helix, 33% strand | Q15843 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.75 | 0.96 | 32 | EDO |
| 2 | 138 | 0.68 | 0.89 | 37 | EDO |
| 3 | 234 | 0.51 | 0.75 | 31 | empty |
| 4 | 94 | 0.38 | 0.76 | 20 | empty |
| 5 | 88 | 0.37 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1489 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1482 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 362 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4F8C · Structure of the CIF:NEDD8 complex - yersinia pseudotuberculosis cycle inhibiting factor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q15843 · AlphaFold monomer V2.0 prediction for NEDD8 (Q15843) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 B1JJZ9
- Every structure of UniProt Q15843
- Elsewhere: RCSB PDB 4F8C · PDBe 4F8C · UniProt B1JJZ9 · UniProt Q15843
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