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UBV.B4R, a dimeric ubiquitin variant binding to BIRC4 ring

Analyse UBV.B4R, a dimeric ubiquitin variant binding to BIRC4 ring in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5O6S
Type: protein
Length: 450 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyubiquitin-B
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E	Polyubiquitin-B	protein	75	19% helix, 39% strand	—
B	Polyubiquitin-B	protein	76	18% helix, 38% strand	—
C	Polyubiquitin-B	protein	75	19% helix, 41% strand	—
F	Polyubiquitin-B	protein	74	15% helix, 43% strand	—

Pockets

3 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	120	0.48	0.79	15	empty
2	158	0.42	0.74	18	empty
3	108	0.40	0.76	19	empty

Interfaces

7 interfaces between chains.

E–F · 2166 Å² buried · 52 hydrogen bonds · protein-protein
C–D · 2095 Å² buried · 52 hydrogen bonds · protein-protein
A–B · 2087 Å² buried · 52 hydrogen bonds · protein-protein
A–C · 394 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 290 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5O6S · UbV.B4R, a dimeric ubiquitin variant binding to BIRC4 RING · 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 5O6S · PDBe 5O6S

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