GL1X · GenesisL1 explorer

MolNFT v1 · #142512 · protein + RNA

Crystal structure of zebra fish Y-box PROTEIN1 (yb-1) cold-shock domain in complex with 6MER M5C RNA

6A6J: “Crystal structure of zebra fish Y-box PROTEIN1 (yb-1) cold-shock domain in complex with 6MER M5C RNA”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #142512 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6A6J
Type
protein + RNA
Length
190 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Zebra fish Y-box PROTEIN1 (yb-1); RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')
UniProt
B5DE31
Ligands
ZN

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, CZebra fish Y-box PROTEIN1 (yb-1)protein907% helix, 50% strandB5DE31
B, DRNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')rna5——

Ligands and binding sites

  • ZN · Zinc ion · metal · 2 copies · chains A, B, C, D

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

Interfaces

4 interfaces between chains.

  • C–D · 610 Ų buried · 10 hydrogen bonds · protein-nucleic
  • A–B · 601 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–C · 193 Ų buried · 2 hydrogen bonds · protein-protein
  • A–D · 16 Ų buried · 0 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

  • 6A6J · Crystal structure of Zebra fish Y-box protein1 (YB-1) Cold-shock domain in complex with… · the same entry in another collection · chain C against C, TM-score 1.00
  • B5DE31 · AlphaFold monomer V2.0 prediction for Y-box-binding protein 1 (B5DE31) · a predicted model of the same protein · chain A against A, TM-score 0.96

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