IL_5J1O_013

3D structure

PDB id

5J1O (explore in PDB, NAKB, or RNA 3D Hub)

Description

Excited state (Bound-like) sampled during RDC restrained Replica-averaged Metadynamics (RAM) simulations of the HIV-1 TAR complexed with cyclic peptide mimetic of Tat

Experimental method

SOLUTION NMR

Resolution

Loop

Sequence

GAUCUG*CUC

Length

9 nucleotides

Bulged bases

5J1O|7|B|C|24

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_5J1O_013 not in the Motif Atlas

Geometric match to IL_4V9F_028

Geometric discrepancy: 0.3885

The information below is about IL_4V9F_028

Detailed Annotation

Major groove platform with extra cWW

Broad Annotation

Major groove platform

Motif group

IL_36931.3

Basepair signature

cWW-cSH-cWW-cWW

Number of instances in this motif group

26

Unit IDs

5J1O|7|B|G|21
5J1O|7|B|A|22
5J1O|7|B|U|23
5J1O|7|B|C|24
5J1O|7|B|U|25
5J1O|7|B|G|26
*
5J1O|7|B|C|39
5J1O|7|B|U|40
5J1O|7|B|C|41

Current chains

Chain B

Apical region (29mer) of the HIV-1 TAR element

Nearby chains

Chain A

Cyclic peptide mimetic of Tat