MolNFT v1 · #128274 · protein
Crystal structure of ZN3-E16V human ubiquitin (hub) mutant adduct, from a solution 70 mm zinc ACETATE/20% V/V TFE/1.3 mm E16V hub
5NLJ · Polyubiquitin-B: “Crystal structure of ZN3-E16V human ubiquitin (hub) mutant adduct, from a solution 70 mm zinc ACETATE/20% V/V…”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.39). MolNFT v1 #128274 on GenesisL1…
- PDB
- 5NLJ
- Type
- protein
- Length
- 214 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-B
- UniProt
- P0CG47
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polyubiquitin-B | protein | 71 | 25% helix, 30% strand | P0CG47 |
| C | Polyubiquitin-B | protein | 72 | 25% helix, 35% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, C, B
- ACT · Acetate ion · additive · 6 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains B
- ETF · Trifluoroethanol · additive · chains B
- EDO · 1,2-ethanediol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 79 | 0.39 | 0.78 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 342 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 308 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5NLJ · Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM… · the same entry in another collection · chain A against A, TM-score 1.00
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 P0CG47
- Elsewhere: RCSB PDB 5NLJ · PDBe 5NLJ · UniProt P0CG47
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