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Structure of S-gna dodecamer

Analyse Structure of S-gna dodecamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5V1L
Type
RNA
Length
44 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')
Ligands
ZTH, SPM, SR
Pockets
3 · best druggability 0.40

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DRNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')rna11——

Ligands and binding sites

  • ZTH · (S)-1'-(2',3'-dihydroxypropyl)-thymine · ligand · 4 copies · chains A, B, C, D
  • SPM · Spermine · ligand · chains A, B
  • SR · Strontium ion · metal · 8 copies · chains A, B, C, D

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11780.400.7322ZTH
2750.290.748empty
3500.250.758empty

Interfaces

5 interfaces between chains.

  • A–B · 662 Ų buried · 46 hydrogen bonds · nucleic-nucleic
  • C–D · 627 Ų buried · 46 hydrogen bonds · nucleic-nucleic
  • B–C · 92 Ų buried · 1 hydrogen bond · nucleic-nucleic
  • A–D · 69 Ų buried · 0 hydrogen bonds · nucleic-nucleic
  • A–C · 15 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

  • 5V1L · Structure of S-GNA dodecamer · the same entry in another collection · chain A against A, TM-score 1.00

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