HL_1YXP_002

3D structure

PDB id

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

Description

HIV-1 DIS RNA subtype F- Zn soaked

Experimental method

X-RAY DIFFRACTION

Resolution

2.4 Å

Loop

Sequence

GAAGUGCACAC

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_1YXP_002 not in the Motif Atlas

Geometric match to HL_4V9F_061

Geometric discrepancy: 0.2434

The information below is about HL_4V9F_061

Detailed Annotation

Pseudoknot geometry

Broad Annotation

No text annotation

Motif group

HL_52651.3

Basepair signature

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

Number of instances in this motif group

31

Unit IDs

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

Current chains

Chain B

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

Nearby chains

Chain A

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