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MolNFT v1 · #137875 · DNA

Crystal structure of inosine-substituted decamer duplex DNA (I4)

5W1Z · DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3'): “Crystal structure of inosine-substituted decamer duplex DNA (I4)”. X-ray diffraction, 2 ligands (NA, MG), 1 pocket (best druggability 0.46). MolNFT v1 #137875 on GenesisL1: 3D…

PDB
5W1Z
Type
DNA
Length
40 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3')
Ligands
NA, MG
Pockets
1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DDNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3')dna10——

Ligands and binding sites

  • NA · Sodium ion · metal · 4 copies · chains A, B, C, D
  • MG · Magnesium ion · metal · 3 copies · chains A, C, D

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11670.460.7719NA

Interfaces

4 interfaces between chains.

  • A–B · 457 Ų buried · 34 hydrogen bonds · nucleic-nucleic
  • C–D · 434 Ų buried · 38 hydrogen bonds · nucleic-nucleic
  • A–D · 124 Ų buried · 1 hydrogen bond · nucleic-nucleic
  • B–C · 64 Ų buried · 1 hydrogen bond · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

  • 5W1Z · Crystal Structure of inosine-substituted decamer duplex DNA (I4) · the same entry in another collection · chain A against A, TM-score 1.00

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