Research workbench
Crystal structure of a vflip-ikkgamma complex: insights into viral activation of the ikk signalosome
Analyse Crystal structure of a vflip-ikkgamma complex: insights into viral activation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CL3
- Type
- protein
- Length
- 454 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orf K13; Nf-kappa-B essential modulator
- UniProt
- P88961, Q9Y6K9
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orf K13 | protein | 172 | 63% helix, 0% strand | P88961 |
| B | Orf K13 | protein | 165 | 65% helix, 0% strand | P88961 |
| D | Nf-kappa-B essential modulator | protein | 59 | 90% helix, 0% strand | Q9Y6K9 |
| E | Nf-kappa-B essential modulator | protein | 58 | 88% helix, 0% strand | Q9Y6K9 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.60 | 0.79 | 39 | empty |
| 2 | 213 | 0.60 | 0.81 | 30 | empty |
| 3 | 81 | 0.32 | 0.73 | 18 | empty |
| 4 | 58 | 0.29 | 0.74 | 11 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1227 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 583 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 546 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 307 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 291 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3CL3 · Crystal Structure of a vFLIP-IKKgamma complex: Insights into viral activation of the IKK… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y6K9 · AlphaFold monomer V2.0 prediction for nf-kappa-B essential modulator (Q9Y6K9) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 P88961
- Every structure of UniProt Q9Y6K9
- Elsewhere: RCSB PDB 3CL3 · PDBe 3CL3 · UniProt P88961 · UniProt Q9Y6K9
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