GL1X · GenesisL1 explorer

MolNFT v1 · #18397 · protein + DNA

Peptide nucleic acid (pna) complexed with DNA

1PNN · Pna (NH2-P(*C*T*C*T*T*C*T*T*C-his-gly-ser-ser-gly-his…: “Peptide nucleic acid (pna) complexed with DNA”. X-ray diffraction, 3 ligands (TPN, CPN, IPN). MolNFT v1 #18397 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
1PNN
Type
protein + DNA
Length
30 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Pna (NH2-P(*C*T*C*T*T*C*T*T*C-his-gly-ser-ser-gly-his- C*T*T*C*T*T*C*T*C)-cooh); DNA…
Ligands
TPN, CPN, IPN

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, CPna (NH2-P(*C*T*C*T*T*C*T*T*C-his-gly-ser-ser-gly-his- C*T*T*C*T*T*C*T*C)-cooh)protein60% helix, 0% strand—
B, DDNA (5'-D(GP*AP*AP*GP*AP*AP*GP*AP*G)-3')dna9——

Ligands and binding sites

  • TPN · 2-aminoethylglycine-carbonylmethylene-thymine · ligand · 18 copies · chains B, D
  • CPN · 2-aminoethylglycine-carbonylmethylene-cytosine · ligand · 16 copies · chains B, D, A, C
  • IPN · 2-aminoethylglycine-carbonylmethylene-5-iodouracil · ligand · 2 copies · chains B, D

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

Interfaces

3 interfaces between chains.

  • A–B · 122 Ų buried · 2 hydrogen bonds · protein-nucleic
  • C–D · 102 Ų buried · 3 hydrogen bonds · protein-nucleic
  • B–D · 73 Ų buried · 2 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

  • 1PNN · Peptide nucleic acid (pna) complexed with DNA · the same entry in another collection · chain B against B, TM-score 1.00

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