Research workbench
Nemo cozi domain in complex with diubiquitin in C2 space group
Analyse Nemo cozi domain in complex with diubiquitin in C2 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZVO
- Type
- protein
- Length
- 471 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubc protein; Nf-kappa-B essential modulator
- UniProt
- Q96C32, O88522
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubc protein | protein | 149 | 23% helix, 36% strand | Q96C32 |
| G | Ubc protein | protein | 146 | 21% helix, 32% strand | Q96C32 |
| B, D | Nf-kappa-B essential modulator | protein | 88 | 92% helix, 0% strand | O88522 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.50 | 0.75 | 41 | empty |
| 2 | 89 | 0.34 | 0.74 | 23 | empty |
| 3 | 82 | 0.31 | 0.73 | 12 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1984 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 671 Ų buried · 7 hydrogen bonds · protein-protein
- G–B · 654 Ų buried · 3 hydrogen bonds · protein-protein
- G–D · 575 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 544 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2ZVO · NEMO CoZi domain in complex with diubiquitin in C2 space group · 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 B 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 Q96C32
- Every structure of UniProt O88522
- Elsewhere: RCSB PDB 2ZVO · PDBe 2ZVO · UniProt Q96C32 · UniProt O88522
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