Research workbench
Crystal structure of ZN1.7-E16V human ubiquitin (hub) mutant adduct, from a solution 70 mm zinc ACETATE/1.3 mm E16V hub
Analyse Crystal structure of ZN1.7-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
- 5NL5
- Type
- protein
- Length
- 216 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 0.35
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Polyubiquitin-B | protein | 72 | 25% helix, 29% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, C
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 | 78 | 0.35 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 348 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 307 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5NL5 · Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70… · 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 5NL5 · PDBe 5NL5 · UniProt P0CG47
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