MolNFT v1 · #114288 · protein

Crystal structure of optineurin uban in complex with linear ubiquitin

5B83 · Tetra ubiquitin: “Crystal structure of optineurin uban in complex with linear ubiquitin”. X-ray diffraction, 8 pockets (best druggability 0.69). MolNFT v1 #114288 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B83
Type: protein
Length: 831 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tetra ubiquitin; Optineurin
UniProt: P0CG48, Q96CV9
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 6 distinct chains · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tetra ubiquitin	protein	302	21% helix, 34% strand	P0CG48
B	Optineurin	protein	59	86% helix, 0% strand	Q96CV9
C	Optineurin	protein	61	87% helix, 0% strand	Q96CV9
D	Tetra ubiquitin	protein	300	21% helix, 35% strand	P0CG48
E	Optineurin	protein	50	84% helix, 0% strand	Q96CV9
F	Optineurin	protein	59	86% helix, 0% strand	Q96CV9

Pockets

8 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	86	0.69	0.93	20	empty
2	159	0.47	0.76	22	empty
3	81	0.39	0.77	18	empty
4	52	0.33	0.78	11	empty
5	95	0.33	0.73	22	empty

Interfaces

7 interfaces between chains.

B–C · 1551 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1485 Å² buried · 12 hydrogen bonds · protein-protein
D–F · 734 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 720 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 544 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5B83 · Crystal structure of Optineurin UBAN in complex with linear ubiquitin · the same entry in another collection · chain F against F, TM-score 1.00
Q96CV9 · AlphaFold monomer V2.0 prediction for optineurin (Q96CV9) · a predicted model of the same protein · chain E against A, TM-score 0.89

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 Q96CV9
Elsewhere: RCSB PDB 5B83 · PDBe 5B83 · UniProt P0CG48 · UniProt Q96CV9

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