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Crystal structure of ZN2.3-hub (human ubiquitin) adduct from a solution 70 mm zinc ACETATE/1.3 mm hub

Analyse Crystal structure of ZN2.3-hub (human ubiquitin) adduct from a solution 70 mm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K7U
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 0.54

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
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
ACT · Acetate ion · additive · 3 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	54	0.54	0.89	20	ACT
2	98	0.39	0.76	22	empty

Interfaces

2 interfaces between chains.

A–B · 353 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 291 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4K7U · Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc… · the same entry in another collection · chain A against A, TM-score 1.00

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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 4K7U · PDBe 4K7U · UniProt P0CG48

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