MolNFT v1 · #124531 · protein

Crystal structure of oxime-linked K6 diubiquitin

5KHY · Polyubiquitin-B: “Crystal structure of oxime-linked K6 diubiquitin”. X-ray diffraction, 2 ligands (ETA, ZN), 2 pockets (best druggability 0.43). MolNFT v1 #124531 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KHY
Type: protein
Length: 148 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyubiquitin-B
UniProt: P0CG47
Ligands: ETA, ZN
Pockets: 2 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyubiquitin-B	protein	73	25% helix, 27% strand	P0CG47
B	Polyubiquitin-B	protein	75	24% helix, 33% strand	P0CG47

Ligands and binding sites

ETA · Ethanolamine · ligand · chains A, B
ZN · Zinc ion · metal · 10 copies · chains A, B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	88	0.43	0.79	20	empty
2	58	0.42	0.82	17	empty

Interfaces

1 interface between chains.

A–B · 358 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).

Compared structures

5KHY · Crystal structure of oxime-linked K6 diubiquitin · 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 5KHY · PDBe 5KHY · UniProt P0CG47

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