MolNFT v1 · #82699 · protein
Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I
3VUW · Polyubiquitin-C: “Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I”. X-ray diffraction, 2 ligands (ZN, K), 3 pockets (best druggability 0.42). MolNFT v1 #82699 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3VUW
- Type
- protein
- Length
- 317 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-C; Tumor necrosis factor alpha-induced protein 3
- UniProt
- P0CG48, P21580
- Ligands
- ZN, K
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polyubiquitin-C | protein | 74 | 24% helix, 34% strand | P0CG48 |
| C | Polyubiquitin-C | protein | 75 | 20% helix, 33% strand | P0CG48 |
| E, G | Tumor necrosis factor alpha-induced protein 3 | protein | 31 | 39% helix, 6% strand | P21580 |
| F | Tumor necrosis factor alpha-induced protein 3 | protein | 32 | 38% helix, 6% strand | P21580 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains C, E, B, F, A, G
- K · Potassium ion · metal · 3 copies · chains E, F, G
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 | 111 | 0.42 | 0.77 | 17 | empty |
| 2 | 86 | 0.41 | 0.78 | 18 | empty |
| 3 | 58 | 0.30 | 0.76 | 15 | empty |
Interfaces
8 interfaces between chains.
- A–G · 625 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 624 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 620 Ų buried · 2 hydrogen bonds · protein-protein
- B–G · 304 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 279 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3VUW · Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I · the same entry in another collection · chain G against G, TM-score 1.00
- P21580 · AlphaFold monomer V2.0 prediction for tumor necrosis factor alpha- induced protein 3… · a predicted model of the same protein · chain E 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 P0CG48
- Every structure of UniProt P21580
- Elsewhere: RCSB PDB 3VUW · PDBe 3VUW · UniProt P0CG48 · UniProt P21580
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