MolNFT v1 · #11001 · protein + DNA

Solution structure of the nucleopeptide [ac-lys-TRP-lys- HSE(P3DGCATCG)-ala]-[P5DCGTAGC]

1J9N · 5'-D(*GP*CP*TP*AP*CP*(PGN))-3': “Solution structure of the nucleopeptide [ac-lys-TRP-lys- HSE(P3*DGCATCG)-ala]-[P5*DCGTAGC]”. Solution nmr, 2 ligands (ACE, HSE). MolNFT v1 #11001 on GenesisL1: 3D structure, binding sites and pockets…

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).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-D(GPCPTPAPCP(PGN))-3'	dna	6	—	—
B	5'-D(CPGPTPAPGPC)-3'	dna	6	—	—
C	Peptide ACE-lys-TRP-lys-hse-ala	protein	4	0% 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 Å² buried · 32 hydrogen bonds · nucleic-nucleic
A–C · 159 Å² buried · 3 hydrogen bonds · protein-nucleic
B–C · 59 Å² 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

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1J9N · PDBe 1J9N

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