Research workbench
Crystal structure of mouse nemo cozi in complex with LYS63-linked di- ubiquitin
Analyse Crystal structure of mouse nemo cozi in complex with LYS63-linked di- ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JSV
- Type
- protein
- Length
- 322 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Nf-kappa-B essential modulator
- UniProt
- P62988, O88522
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 76 | 24% helix, 33% strand | P62988 |
| B | Ubiquitin | protein | 77 | 19% helix, 34% strand | P62988 |
| C | Nf-kappa-B essential modulator | protein | 83 | 92% helix, 0% strand | O88522 |
| D | Nf-kappa-B essential modulator | protein | 86 | 94% helix, 0% strand | O88522 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.48 | 0.73 | 27 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2185 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 571 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 133 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 56 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 3JSV · Crystal structure of mouse NEMO CoZi in complex with Lys63-linked di-ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- O88522 · AlphaFold monomer V2.0 prediction for nf-kappa-B essential modulator (O88522) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 P62988
- Every structure of UniProt O88522
- Elsewhere: RCSB PDB 3JSV · PDBe 3JSV · UniProt P62988 · UniProt O88522
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