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Crystal structure of ZN2-E16V human ubiquitin (hub) mutant adduct, from a solution 35 mm zinc ACETATE/10% V/V TFE/1.3 mm E16V hub
Analyse Crystal structure of ZN2-E16V human ubiquitin (hub) mutant adduct, from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NLI
- Type
- protein
- Length
- 220 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-C
- UniProt
- P0CG48
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polyubiquitin-C | protein | 74 | 24% helix, 28% strand | P0CG48 |
| C | Polyubiquitin-C | protein | 72 | 25% helix, 35% strand | P0CG48 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C, B
- ACT · Acetate ion · additive · 5 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
- ETF · Trifluoroethanol · additive · chains B
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 | 77 | 0.38 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 360 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 301 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5NLI · Crystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM… · the same entry in another collection · chain B against B, 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 P0CG48
- Elsewhere: RCSB PDB 5NLI · PDBe 5NLI · UniProt P0CG48
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