MolNFT v1 · #53980 · protein + RNA

Crystal structure of the core mago-Y14-EIF4AIII-barentsz- UPF3B assembly shows how the ejc is bridged to the nmd machinery

2XB2 · Eukaryotic initiation factor 4A-III: “Crystal structure of the core mago-Y14-EIF4AIII-barentsz- UPF3B assembly shows how the ejc is bridged to the…”. X-ray diffraction, 2 ligands (ANP, MG), 20 pockets (best druggability 0.81).…

PDB: 2XB2
Type: protein + RNA
Length: 1,409 residues
Chains: 13
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eukaryotic initiation factor 4A-III; Protein mago nashi homolog; RNA-binding protein 8A…
EC: 3.6.1.-
UniProt: P38919, P61326, Q9Y5S9, Q9BZI7, O15234
Ligands: ANP, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 10 distinct chains · 32% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, X	Eukaryotic initiation factor 4A-III (EC 3.6.1.-)	protein	390	41% helix, 16% strand	P38919
C, Y	Protein mago nashi homolog	protein	143	36% helix, 34% strand	P61326
D, Z	RNA-binding protein 8A	protein	89	22% helix, 35% strand	Q9Y5S9
E	RNA poly-U-ribonucleotide	rna	8	—	—
F	Putative regulator of nonsense transcripts 3B	protein	3	0% helix, 0% strand	—
G	Regulator of nonsense transcripts 3B	protein	15	0% helix, 7% strand	Q9BZI7
R	RNA poly-U-ribonucleotide	rna	7	—	—
S	Protein CASC3	protein	57	12% helix, 0% strand	O15234
T	Protein CASC3	protein	59	17% helix, 0% strand	O15234
U	Regulator of nonsense transcripts 3B	protein	16	0% helix, 6% strand	Q9BZI7

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, X
MG · Magnesium ion · metal · 2 copies · chains A, X

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	821	0.81	0.84	79	empty
2	775	0.78	0.82	64	empty
3	343	0.74	0.86	45	empty
4	361	0.73	0.84	41	empty
5	230	0.69	0.86	40	empty

Interfaces

23 interfaces between chains.

S–X · 2247 Å² buried · 39 hydrogen bonds · protein-protein
A–T · 2244 Å² buried · 35 hydrogen bonds · protein-protein
X–Y · 1695 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 1687 Å² buried · 38 hydrogen bonds · protein-protein
Y–Z · 1264 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

2XB2 · Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the EJC… · the same entry in another collection · chain Z against Z, TM-score 1.00

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 P38919
Every structure of UniProt P61326
Every structure of UniProt Q9Y5S9
Every structure of UniProt Q9BZI7
Every structure of UniProt O15234
Elsewhere: RCSB PDB 2XB2 · PDBe 2XB2 · UniProt P38919 · UniProt P61326 · UniProt Q9Y5S9 · UniProt Q9BZI7 · UniProt O15234

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