IL_1JZV_004

3D structure

PDB id

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

Description

Crystal structure of a bulged RNA from the SL2 stem-loop of the HIV-1 psi-RNA

Experimental method

X-RAY DIFFRACTION

Resolution

1.7 Å

Loop

Sequence

GGC*G(5IC)C

Length

6 nucleotides

Bulged bases

None detected

QA status

Self-complementary:

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_1JZV_004 not in the Motif Atlas

Geometric match to IL_3SZX_003

Geometric discrepancy: 0.1169

The information below is about IL_3SZX_003

Detailed Annotation

Isolated non-canonical cWW pair

Broad Annotation

Isolated non-canonical cWW pair

Motif group

IL_01003.2

Basepair signature

cWW-cWW-cWW

Number of instances in this motif group

213

Unit IDs

1JZV|1|C|G|21
1JZV|1|C|G|22
1JZV|1|C|C|23
*
1JZV|1|D|G|35
1JZV|1|D|5IC|36
1JZV|1|D|C|37

Current chains

Chain C

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

Chain D

5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'

Nearby chains

Chain A

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

Chain B

5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'