MolNFT v1 · #28588 · protein

X-ray crystal structure of a chemically synthesized ubiquitin

1YIW: “X-ray crystal structure of a chemically synthesized ubiquitin”. X-ray diffraction, 2 ligands (CD, CL), 4 pockets (best druggability 0.53). MolNFT v1 #28588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YIW
Type: protein
Length: 216 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin
Ligands: CD, CL
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ubiquitin	protein	71	25% helix, 30% strand	—
C	Ubiquitin	protein	74	24% helix, 34% strand	—

Ligands and binding sites

CD · Cadmium ion · metal · 17 copies · chains A, B, C
CL · Chloride ion · ion · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 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	185	0.53	0.79	30	CD, CL
2	94	0.35	0.74	18	empty
3	80	0.34	0.75	11	empty
4	101	0.34	0.73	15	empty

Interfaces

3 interfaces between chains.

A–B · 225 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 224 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 213 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1YIW · X-ray Crystal Structure of a Chemically Synthesized Ubiquitin · 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
Elsewhere: RCSB PDB 1YIW · PDBe 1YIW

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