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LYS27-linked triubiquitin

Analyse LYS27-linked triubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JBY
Type: protein
Length: 418 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; D-ubiquitin
UniProt: P0CG47
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 28% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Ubiquitin	protein	73	26% helix, 34% strand	P0CG47
B, D	D-ubiquitin	protein	67	27% helix, 31% strand	—
C	Ubiquitin	protein	72	31% helix, 33% strand	P0CG47
F	D-ubiquitin	protein	66	27% helix, 30% strand	—

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	287	0.82	0.94	39	empty
2	648	0.76	0.82	87	empty
3	79	0.41	0.79	14	empty
4	94	0.39	0.77	16	empty
5	85	0.38	0.77	19	empty

Interfaces

12 interfaces between chains.

A–D · 442 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 437 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 413 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 384 Å² buried · 8 hydrogen bonds · protein-protein
C–F · 383 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 188 d-amino, 3 modified (D-amino acid, nonstandard).

Compared structures

5JBY · Lys27-linked triubiquitin · the same entry in another collection · chain F against F, TM-score 1.00
P0CG47 · AlphaFold monomer V2.0 prediction for polyubiquitin-B (P0CG47) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 5JBY · PDBe 5JBY · UniProt P0CG47

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