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Crystal structure of ZN3-HUB(HUMAN ubiquitin) adduct from a solution 100 mm zinc ACETATE/1.3 mm hub
Analyse Crystal structure of ZN3-HUB(HUMAN ubiquitin) adduct from a solution 100 mm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K7W
- Type
- protein
- Length
- 216 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- EC
- 6.3.2.19
- UniProt
- P0CG48
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ubiquitin (EC 6.3.2.19) | protein | 72 | 25% helix, 29% strand | P0CG48 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, C, B
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.58 | 0.89 | 21 | empty |
| 2 | 118 | 0.41 | 0.76 | 23 | ZN |
Interfaces
2 interfaces between chains.
- A–B · 379 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 293 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4K7W · Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc… · 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 P0CG48
- Elsewhere: RCSB PDB 4K7W · PDBe 4K7W · UniProt P0CG48
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