MolNFT v1 · #97235 · protein
Crystal structure of ZN2-hub (human ubiquitin) adduct from a solution 35 mm zinc ACETATE/1.3 mm hub
4K7S: “Crystal structure of ZN2-hub (human ubiquitin) adduct from a solution 35 mm zinc ACETATE/1.3 mm hub”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.50). MolNFT v1 #97235 on GenesisL1: 3D structure, binding sites…
- PDB
- 4K7S
- Type
- protein
- Length
- 214 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 0.50
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin (EC 6.3.2.19) | protein | 70 | 26% helix, 30% strand | P0CG48 |
| B, C | Ubiquitin (EC 6.3.2.19) | protein | 72 | 25% helix, 32% strand | P0CG48 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
- ACT · Acetate ion · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.50 | 0.86 | 19 | ACT |
| 2 | 71 | 0.34 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 303 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4K7S · Crystal structure of Zn2-hUb (human ubiquitin) adduct from a solution 35 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 4K7S · PDBe 4K7S · UniProt P0CG48
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