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Crystal structure of YBX1 csd with M5C RNA

Analyse Crystal structure of YBX1 csd with M5C RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KTC
Type: protein + RNA
Length: 78 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclease-sensitive element-binding protein 1; RNA (5'-R(P*GP*(5MC)P*CP*U)-3')
UniProt: P67809

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclease-sensitive element-binding protein 1	protein	74	4% helix, 58% strand	P67809
V	RNA (5'-R(PGP(5MC)PCPU)-3')	rna	4	—	—

Interfaces

1 interface between chains.

A–V · 562 Å² buried · 10 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

6KTC · Crystal structure of YBX1 CSD with m5C RNA · the same entry in another collection · chain A against A, TM-score 1.00
P67809 · AlphaFold monomer V2.0 prediction for Y-box-binding protein 1 (P67809) · a predicted model of the same protein · chain A against A, TM-score 0.94

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P67809
Elsewhere: RCSB PDB 6KTC · PDBe 6KTC · UniProt P67809

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