MolNFT v1 · #178066 · protein + RNA

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

7F3K · Y-box-binding protein 2: “Crystal structure of human YBX2 csd in complex with M5C RNA in space group P21212”. X-ray diffraction, 1 ligand (SO4). MolNFT v1 #178066 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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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