MolNFT v1 · #188501 · protein
Crystal structure of nemo cozi in complex with hoip NZF1 and linear diubiquitin
7TV4 · Nf-kappa-B essential modulator: “Crystal structure of nemo cozi in complex with hoip NZF1 and linear diubiquitin”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.42). MolNFT v1 #188501 on GenesisL1: 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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