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Zipcode-binding-protein-1 KH3KH4(DD) domains in complex with the KH3 RNA target

Analyse Zipcode-binding-protein-1 KH3KH4(DD) domains in complex with the KH3 RNA target in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2N8L
Type: protein + RNA
Length: 199 residues
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Insulin-like growth factor 2 mRNA-binding protein 1; RNA…
UniProt: O42254
Pockets: 2 · best druggability 0.59

Structure

solution nmr · 2 distinct chains · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Insulin-like growth factor 2 mRNA-binding protein 1	protein	191	41% helix, 19% strand	O42254
B	RNA (5'-R(PGPCPAPCPAPCPCPC)-3')	rna	8	—	—

Pockets

2 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	58	0.59	0.90	15	empty
2	59	0.28	0.74	12	empty

Interfaces

1 interface between chains.

A–B · 478 Å² buried · 18 hydrogen bonds · protein-nucleic

Compared structures

2N8L · Zipcode-binding-protein-1 KH3KH4(DD) domains in complex with the KH3 RNA target · the same entry in another collection · chain A against A, TM-score 1.00
O42254 · AlphaFold monomer V2.0 prediction for insulin-like growth factor 2 mRNA-binding protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.73

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 O42254
Elsewhere: RCSB PDB 2N8L · PDBe 2N8L · UniProt O42254

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