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MolNFT v1 · #175835 · DNA

The tba-PB2+ complex in P41212 space group

7D32 · DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)- 3'): “The tba-PB2+ complex in P41212 space group”. X-ray diffraction, 1 ligand (PB), 2 pockets (best druggability 0.34). MolNFT v1 #175835 on GenesisL1: 3D structure, binding…

PDB
7D32
Type
DNA
Length
90 nucleotides
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)- 3')
Ligands
PB
Pockets
2 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D, E, FDNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)- 3')dna15——

Ligands and binding sites

  • PB · Lead (II) ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1890.340.7511empty
2700.290.7414empty

Interfaces

5 interfaces between chains.

  • A–B · 742 Ų buried · 28 hydrogen bonds · nucleic-nucleic
  • C–D · 738 Ų buried · 29 hydrogen bonds · nucleic-nucleic
  • E–F · 723 Ų buried · 32 hydrogen bonds · nucleic-nucleic
  • B–C · 313 Ų buried · 3 hydrogen bonds · nucleic-nucleic
  • B–E · 21 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

  • 7D32 · The TBA-Pb2+ complex in P41212 space group · the same entry in another collection · chain A against A, TM-score 1.00

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