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Crystal structure of the mouse HOIL1-L-nzf in complex with linear di- ubiquitin

Analyse Crystal structure of the mouse HOIL1-L-nzf in complex with linear di- ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3B08
Type: protein
Length: 836 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyubiquitin-C; Ranbp-type and C3HC4-type zinc finger-containing protein 1
UniProt: P0CG48, Q9WUB0
Ligands: GLC, ZN
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 6 distinct chains · 24% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Polyubiquitin-C	protein	151	24% helix, 36% strand	P0CG48
B	Ranbp-type and C3HC4-type zinc finger-containing protein 1	protein	58	24% helix, 10% strand	Q9WUB0
E, H	Ranbp-type and C3HC4-type zinc finger-containing protein 1	protein	59	24% helix, 10% strand	Q9WUB0
G	Polyubiquitin-C	protein	150	22% helix, 36% strand	P0CG48
J	Polyubiquitin-C	protein	149	24% helix, 36% strand	P0CG48
K	Ranbp-type and C3HC4-type zinc finger-containing protein 1	protein	59	27% helix, 10% strand	Q9WUB0

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 4 copies · chains H, G, K, J
ZN · Zinc ion · metal · 4 copies · chains B, E, H, K

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	322	0.69	0.83	56	GLC
2	115	0.66	0.89	22	empty
3	215	0.65	0.83	46	empty
4	105	0.64	0.89	18	empty
5	162	0.59	0.83	28	empty

Interfaces

12 interfaces between chains.

J–K · 942 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 906 Å² buried · 8 hydrogen bonds · protein-protein
B–G · 855 Å² buried · 9 hydrogen bonds · protein-protein
D–K · 836 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 834 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3B08 · Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin · the same entry in another collection · chain K against K, TM-score 1.00
Q9WUB0 · AlphaFold monomer V2.0 prediction for ranbp-type and C3HC4-type zinc finger-containing… · a predicted model of the same protein · chain K against A, TM-score 0.78

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 P0CG48
Every structure of UniProt Q9WUB0
Elsewhere: RCSB PDB 3B08 · PDBe 3B08 · UniProt P0CG48 · UniProt Q9WUB0

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