IL_2KDQ_011

3D structure

PDB id

2KDQ (explore in PDB, NAKB, or RNA 3D Hub)

Description

Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimic of Tat protein

Experimental method

SOLUTION NMR

Resolution

Loop

Sequence

AUCUG*CU

Length

7 nucleotides

Bulged bases

2KDQ|9|B|C|24, 2KDQ|9|B|U|25

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_2KDQ_011 not in the Motif Atlas

Geometric match to IL_4V88_392

Geometric discrepancy: 0.2409

The information below is about IL_4V88_392

Detailed Annotation

Multiple bulged bases

Broad Annotation

No text annotation

Motif group

IL_82107.1

Basepair signature

cWW-cWW

Number of instances in this motif group

34

Unit IDs

2KDQ|9|B|A|22
2KDQ|9|B|U|23
2KDQ|9|B|C|24
2KDQ|9|B|U|25
2KDQ|9|B|G|26
*
2KDQ|9|B|C|39
2KDQ|9|B|U|40

Current chains

Chain B

HIV-1 TAR RNA

Nearby chains

Chain A

L-22 CYCLIC PEPTIDE