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Calcium bound to the holliday junction sequence D(TCGGCGCCGA)4

Analyse Calcium bound to the holliday junction sequence D(TCGGCGCCGA)4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3GNK
Type
DNA
Length
40 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
Ligands
CA, NA
Pockets
2 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'dna10——

Ligands and binding sites

  • CA · Calcium ion · metal · 2 copies · chains A, D, C
  • NA · Sodium ion · metal · 2 copies · chains A, B, D

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
12290.460.7418NA
21730.420.7415empty

Interfaces

6 interfaces between chains.

  • C–D · 324 Ų buried · 28 hydrogen bonds · nucleic-nucleic
  • A–B · 318 Ų buried · 29 hydrogen bonds · nucleic-nucleic
  • B–D · 226 Ų buried · 3 hydrogen bonds · nucleic-nucleic
  • A–D · 225 Ų buried · 23 hydrogen bonds · nucleic-nucleic
  • B–C · 212 Ų buried · 21 hydrogen bonds · nucleic-nucleic

Compared structures

  • 3GNK · Calcium bound to the Holliday junction sequence d(TCGGCGCCGA)4 · the same entry in another collection · chain B against B, TM-score 1.00

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