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Crystal structure of human YBX2 csd in complex with M5C RNA in space group P21212

Analyse Crystal structure of human YBX2 csd in complex with M5C RNA in space group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7F3K
Type: protein + RNA
Length: 96 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Y-box-binding protein 2; RNA (5'-R(*UP*CP*AP*UP*(5MC)P*U)-3')
UniProt: Q9Y2T7
Ligands: SO4

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Y-box-binding protein 2	protein	90	7% helix, 46% strand	Q9Y2T7
B	RNA (5'-R(UPCPAPUP(5MC)PU)-3')	rna	6	—	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A

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

Interfaces

1 interface between chains.

A–B · 693 Å² buried · 13 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

7F3K · Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P21212 · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y2T7 · AlphaFold monomer V2.0 prediction for Y-box-binding protein 2 (Q9Y2T7) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9Y2T7
Elsewhere: RCSB PDB 7F3K · PDBe 7F3K · UniProt Q9Y2T7

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