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Structure of a DNA analog of the primer for HIV-1 rt second strand synthesis

Analyse Structure of a DNA analog of the primer for HIV-1 rt second strand synthesis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 307D
Type: DNA
Length: 60 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'); DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')
Pockets: 1 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	DNA (5'-D(CPAPAPAPGPAPAPAPAPG)-3')	dna	10	—	—
B, D, F	DNA (5'-D(CPTPTPTPTPCPTPTPTPG)-3')	dna	10	—	—

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	156	0.39	0.73	16	empty

Interfaces

5 interfaces between chains.

C–D · 452 Å² buried · 45 hydrogen bonds · nucleic-nucleic
A–B · 445 Å² buried · 41 hydrogen bonds · nucleic-nucleic
E–F · 442 Å² buried · 51 hydrogen bonds · nucleic-nucleic
B–D · 64 Å² buried · 1 hydrogen bond · nucleic-nucleic
A–C · 43 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Compared structures

307D · Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis · 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 307D · PDBe 307D

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