IL_6D2U_014

3D structure

PDB id

6D2U (explore in PDB, NAKB, or RNA 3D Hub)

Description

Solution structure of a ultra-high affinity macrocycle bound to HIV-1 TAR RNA

Experimental method

SOLUTION NMR

Resolution

Loop

Sequence

AUCUG*CU

Length

7 nucleotides

Bulged bases

6D2U|10|B|C|24, 6D2U|10|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_6D2U_014 not in the Motif Atlas

Geometric match to IL_5LYS_007

Geometric discrepancy: 0.2186

The information below is about IL_5LYS_007

Detailed Annotation

Major groove intercalation

Broad Annotation

Major groove intercalation

Motif group

IL_77710.2

Basepair signature

cWW-L-cWW

Number of instances in this motif group

27

Unit IDs

6D2U|10|B|A|22
6D2U|10|B|U|23
6D2U|10|B|C|24
6D2U|10|B|U|25
6D2U|10|B|G|26
*
6D2U|10|B|C|39
6D2U|10|B|U|40

Current chains

Chain B

RNA (29-MER)

Nearby chains

Chain A

DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO