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Solution structure of the nucleopeptide [ac-lys-TRP-lys- HSE(P3*DGCATCG)-ala]-[P5*DCGTAGC]

Analyse Solution structure of the nucleopeptide [ac-lys-TRP-lys… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1J9N
Type
protein + DNA
Length
16 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*GP*CP*TP*AP*CP*(PGN))-3'; 5'-D(*CP*GP*TP*AP*GP*C)-3'; Peptide…
Ligands
ACE, HSE

Structure

solution nmr · 3 distinct chains · 0% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A5'-D(*GP*CP*TP*AP*CP*(PGN))-3'dna6——
B5'-D(*CP*GP*TP*AP*GP*C)-3'dna6——
CPeptide ACE-lys-TRP-lys-hse-alaprotein40% helix, 0% strand—

Ligands and binding sites

  • ACE · Acetyl group · ligand · chains C
  • HSE · L-homoserine · ligand · chains A, C

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

Interfaces

3 interfaces between chains.

  • A–B · 271 Ų buried · 32 hydrogen bonds · nucleic-nucleic
  • A–C · 159 Ų buried · 3 hydrogen bonds · protein-nucleic
  • B–C · 59 Ų buried · 0 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 covalent, 1 modified (covalent ligand, nucleotide modification).

Compared structures

  • 1J9N · Solution Structure of the Nucleopeptide [AC-LYS-TRP-LYS-HSE(p3*dGCATCG)-ALA]-[p5*dCGTAGC] · the same entry in another collection · chain A against A, TM-score 1.00

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