MolNFT v1 · #57188 · RNA

3'-DNA-RNA-5' junction formed during initiation of minus- strand synthesis of HIV replication

398D · RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3'): “3'-DNA-RNA-5' junction formed during initiation of minus- strand synthesis of HIV replication”. X-ray diffraction. MolNFT v1 #57188 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 398D
Type: RNA
Length: 32 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3'); DNA/RNA (5'-R(*GP*CP*CP*AP)-D(*CP*TP*GP*C)-3')

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	RNA (5'-R(GPCPAPGPUPGPGPC)-3')	rna	8	—	—
B, D	DNA/RNA (5'-R(GPCPCPAP)-D(CPTPGPC)-3')	rna	8	—	—

Interfaces

5 interfaces between chains.

A–B · 387 Å² buried · 36 hydrogen bonds · nucleic-nucleic
C–D · 385 Å² buried · 33 hydrogen bonds · nucleic-nucleic
A–C · 86 Å² buried · 3 hydrogen bonds · nucleic-nucleic
B–D · 84 Å² buried · 3 hydrogen bonds · nucleic-nucleic
B–C · 82 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Compared structures

398D · 3'-DNA-RNA-5' junction formed during initiation of minus-strand synthesis of HIV… · 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 398D · PDBe 398D

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