Research workbench
Crystal structure of nemo cozi in complex with hoip NZF1 and linear diubiquitin
Analyse Crystal structure of nemo cozi in complex with hoip NZF1 and linear diubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TV4
- Type
- protein
- Length
- 486 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nf-kappa-B essential modulator; Polyubiquitin-C; E3 ubiquitin-protein ligase RNF31
- EC
- 2.3.2.31
- UniProt
- Q9Y6K9, P0CG48, Q96EP0
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Nf-kappa-B essential modulator | protein | 81 | 90% helix, 0% strand | Q9Y6K9 |
| C | Polyubiquitin-C | protein | 147 | 20% helix, 27% strand | P0CG48 |
| D | Nf-kappa-B essential modulator | protein | 79 | 84% helix, 0% strand | Q9Y6K9 |
| G | Polyubiquitin-C | protein | 152 | 17% helix, 33% strand | P0CG48 |
| K | E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31) | protein | 27 | 0% helix, 15% strand | Q96EP0 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.42 | 0.80 | 15 | empty |
| 2 | 160 | 0.40 | 0.73 | 18 | empty |
| 3 | 88 | 0.33 | 0.73 | 18 | empty |
Interfaces
7 interfaces between chains.
- B–D · 2179 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 697 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 627 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 597 Ų buried · 12 hydrogen bonds · protein-protein
- D–G · 536 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7TV4 · Crystal structure of NEMO CoZi in complex with HOIP NZF1 and linear diubiquitin · the same entry in another collection · chain K against K, 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 0.87
- Q96EP0 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF31 (Q96EP0) · a predicted model of the same protein · chain K against A, TM-score 0.76
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 Q9Y6K9
- Every structure of UniProt P0CG48
- Every structure of UniProt Q96EP0
- Elsewhere: RCSB PDB 7TV4 · PDBe 7TV4 · UniProt Q9Y6K9 · UniProt P0CG48 · UniProt Q96EP0
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