HL_1XPF_002

3D structure

PDB id

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

Description

HIV-1 subtype A genomic RNA Dimerization Initiation Site

Experimental method

X-RAY DIFFRACTION

Resolution

2.3 Å

Loop

Sequence

GAGGUGCACAC

Length

11 nucleotides

Bulged bases

None detected

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

HL_1XPF_002 not in the Motif Atlas

Geometric match to HL_3IGI_005

Geometric discrepancy: 0.258

The information below is about HL_3IGI_005

Detailed Annotation

Pseudoknot geometry

Broad Annotation

No text annotation

Motif group

HL_52651.1

Basepair signature

cWW-F-F-F-F-F-F

Number of instances in this motif group

27

Unit IDs

1XPF|1|B|G|7
1XPF|1|B|A|8
1XPF|1|B|G|9
1XPF|1|B|G|10
1XPF|1|B|U|11
1XPF|1|B|G|12
1XPF|1|B|C|13
1XPF|1|B|A|14
1XPF|1|B|C|15
1XPF|1|B|A|16
1XPF|1|B|C|17

Current chains

Chain B

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

Nearby chains

Chain A

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