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Crystal structure of RNA:DNA dodecamer corresponding to HIV-1 polypurine tract, at 1.6 a resolution.

Analyse Crystal structure of RNA:DNA dodecamer corresponding to HIV-1 polypurine tract… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SSF
Type: DNA + RNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*GP*G)-3'; 5'-D(*CP*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*A)-3'
Ligands: MG
Pockets: 1 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-R(UPAPAPAPAPGPAPAPAPAPGPG)-3'	rna	12	—	—
B	5'-D(CPCPTPTPTPTPCPTPTPTPTPA)-3'	dna	12	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	199	0.43	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 525 Å² buried · 43 hydrogen bonds · nucleic-nucleic

Compared structures

3SSF · Crystal structure of RNA:DNA dodecamer corresponding to HIV-1 polypurine tract, at 1.6 A… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3SSF · PDBe 3SSF

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