Research workbench

NEMO/IKKb association domain structure

Analyse NEMO/IKKb association domain structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BRV
Type: protein
Length: 204 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: Inhibitor of nuclear factor kappa-B kinase subunit beta; NF-kappa-B essential modulator
EC: 2.7.11.10
UniProt: O14920, Q9Y6K9
Pockets: 1 · best druggability 0.69

Structure

x-ray diffraction · resolution 2.2 · 4 distinct chains · 89% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inhibitor of nuclear factor kappa-B kinase subunit beta (EC 2.7.11.10)	protein	39	77% helix, 0% strand	O14920
B	NF-kappa-B essential modulator	protein	61	97% helix, 0% strand	Q9Y6K9
C	Inhibitor of nuclear factor kappa-B kinase subunit beta (EC 2.7.11.10)	protein	42	79% helix, 0% strand	O14920
D	NF-kappa-B essential modulator	protein	62	95% helix, 0% strand	Q9Y6K9

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	99	0.69	0.92	18	empty

Interfaces

6 interfaces between chains.

B–C · 978 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 954 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 930 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 922 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 892 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3BRV · NEMO/IKKB association domain structure · the same entry in another collection · chain D against D, TM-score 1.00
Q9Y6K9 · AlphaFold monomer V2.0 prediction for nf-kappa-B essential modulator (Q9Y6K9) · a predicted model of the same protein · chain B against A, TM-score 0.91
O14920 · AlphaFold monomer V2.0 prediction for inhibitor of nuclear factor kappa-B kinase subunit… · a predicted model of the same protein · chain A 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 O14920
Every structure of UniProt Q9Y6K9
Elsewhere: RCSB PDB 3BRV · PDBe 3BRV · UniProt O14920 · UniProt Q9Y6K9

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.