IL_1OSW_002

3D structure

PDB id

1OSW (explore in PDB, NAKB, or RNA 3D Hub)

Description

The Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop

Experimental method

SOLUTION NMR

Resolution

Loop

Sequence

GGC*GAGGC

Length

8 nucleotides

Bulged bases

1OSW|2|A|G|18

QA status

Valid loop

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

IL_1OSW_002 not in the Motif Atlas

Geometric match to IL_5TBW_087

Geometric discrepancy: 0.373

The information below is about IL_5TBW_087

Detailed Annotation

Major groove platform with extra pair

Broad Annotation

Major groove platform

Motif group

IL_63450.5

Basepair signature

cWW-cHS-cWW-cWW-cWW

Number of instances in this motif group

7

Unit IDs

1OSW|2|A|G|4
1OSW|2|A|G|5
1OSW|2|A|C|6
*
1OSW|2|A|G|15
1OSW|2|A|A|16
1OSW|2|A|G|17
1OSW|2|A|G|18
1OSW|2|A|C|19

Current chains

Chain A

5'-R(*GP*GP*AP*GP*GP*CP*GP*CP*UP*AP*CP*GP*GP*CP*GP*AP*GP*GP*CP*UP*CP*CP*A)-3'

Nearby chains