MolNFT v1 · #158995 · protein

Structure of whb in complex with ubiquitin variant

6OB1: “Structure of whb in complex with ubiquitin variant”. Solution nmr, 3 pockets (best druggability 0.45). MolNFT v1 #158995 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OB1
Type: protein
Length: 240 residues
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; Anaphase-promoting complex subunit 2
UniProt: Q9UJX6
Pockets: 3 · best druggability 0.45

Structure

solution nmr · 3 distinct chains · 33% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin	protein	75	20% helix, 43% strand	—
B	Ubiquitin	protein	75	20% helix, 44% strand	—
C	Anaphase-promoting complex subunit 2	protein	90	53% helix, 6% strand	Q9UJX6

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	135	0.45	0.76	20	empty
2	61	0.39	0.80	13	empty
3	65	0.33	0.76	14	empty

Interfaces

3 interfaces between chains.

A–B · 2076 Å² buried · 55 hydrogen bonds · protein-protein
A–C · 662 Å² buried · 1 hydrogen bond · protein-protein
B–C · 186 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6OB1 · Structure of WHB in complex with Ubiquitin Variant · the same entry in another collection · chain A against A, TM-score 1.00
Q9UJX6 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 2 (Q9UJX6) · a predicted model of the same protein · chain C against A, TM-score 0.72

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 Q9UJX6
Elsewhere: RCSB PDB 6OB1 · PDBe 6OB1 · UniProt Q9UJX6

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