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MolNFT v1 · #18237 · DNA

Esperamicin A1-DNA complex, NMR, 4 structures

1PIK · DNA (5'-D(C*GP*GP*AP*TP*CP*CP*GP)-3'): “Esperamicin A1-DNA complex, NMR, 4 structures”. Solution nmr, 6 ligands (DAG, MAT, DPA). MolNFT v1 #18237 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
1PIK
Type
DNA
Length
16 nucleotides
Chains
2
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(C*GP*GP*AP*TP*CP*CP*GP)-3')
Ligands
DAG, MAT, DPA, TMR, DLF, MTC

Structure

solution nmr · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA (5'-D(C*GP*GP*AP*TP*CP*CP*GP)-3')dna8——

Ligands and binding sites

  • DAG · 4-amino-4,6-dideoxy-beta-D-glucopyranose · ligand · chains A, B
  • MAT · 2,4-dideoxy-3-O-methyl-4-(propan-2-ylamino)-alpha-L-threo-pentopyranose · ligand · chains A
  • DPA · 4,5-dimethoxy-N-(2'-methoxypropenoyl anthranilate) · ligand · chains A, B
  • TMR · 2,6-dideoxy-4-S-methyl-4-thio-beta-D-ribo-hexopyranose · ligand · chains A, B
  • DLF · 2-deoxy-alpha-L-fucopyranose · ligand · chains A, B
  • MTC · [1,8-dihydroxy-11-oxo-13-(2-methyltrithio-ethylidene)-bicyclo[7.3.1]trideca-4,9-diene-2,6-diyn-10-yl]-carbamic acid methyl ester · ligand · chains A, B

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

Interfaces

1 interface between chains.

  • A–B · 409 Ų buried · 33 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1PIK · Esperamicin A1-DNA complex, NMR, 4 structures · the same entry in another collection · chain A against A, TM-score 1.00

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