MolNFT v1 · #96684 · protein

Crystal structure of a complex of NOD1 card and ubiquitin

4JQW · Nucleotide-binding oligomerization domain-containing…: “Crystal structure of a complex of NOD1 card and ubiquitin”. X-ray diffraction, 1 ligand (PO4), 1 pocket (best druggability 0.35). MolNFT v1 #96684 on GenesisL1: 3D structure…

PDB: 4JQW
Type: protein
Length: 165 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleotide-binding oligomerization domain-containing protein 1; Polyubiquitin-C
UniProt: Q9Y239, P0CG48
Ligands: PO4
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleotide-binding oligomerization domain-containing protein 1	protein	92	77% helix, 0% strand	Q9Y239
C	Polyubiquitin-C	protein	73	25% helix, 36% strand	P0CG48

Ligands and binding sites

PO4 · Phosphate ion · ion · chains C

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	95	0.35	0.74	13	empty

Interfaces

1 interface between chains.

A–C · 509 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (artifact).

Compared structures

4JQW · Crystal Structure of a Complex of NOD1 CARD and Ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y239 · AlphaFold monomer V2.0 prediction for nucleotide-binding oligomerization… · a predicted model of the same protein · chain A 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 Q9Y239
Every structure of UniProt P0CG48
Elsewhere: RCSB PDB 4JQW · PDBe 4JQW · UniProt Q9Y239 · UniProt P0CG48

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