IL_1VQM_104

3D structure

PDB id

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

Description

The structure of the transition state analogue 'DAN' bound to the large ribosomal subunit of haloarcula marismortui

Experimental method

X-RAY DIFFRACTION

Resolution

2.3 Å

Loop

Sequence

GGAGUAC*GGAAAC

Length

13 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

IL_1VQM_104 not in the Motif Atlas

Homologous match to IL_4V9F_106

Geometric discrepancy: 0.0385

The information below is about IL_4V9F_106

Detailed Annotation

7x6 Sarcin-Ricin; G-bulge

Broad Annotation

Sarcin-Ricin; G-bulge

Motif group

IL_02666.1

Basepair signature

cWW-tSH-tHH-cSH-tWH-tHS-cWW

Number of instances in this motif group

17

Unit IDs

1VQM|1|9|G|3075
1VQM|1|9|G|3076
1VQM|1|9|A|3077
1VQM|1|9|G|3078
1VQM|1|9|U|3079
1VQM|1|9|A|3080
1VQM|1|9|C|3081
*
1VQM|1|9|G|3101
1VQM|1|9|G|3102
1VQM|1|9|A|3103
1VQM|1|9|A|3104
1VQM|1|9|A|3105
1VQM|1|9|C|3106

Current chains

Chain 9

5S ribosomal RNA

Nearby chains

Chain 0

Large subunit ribosomal RNA; LSU rRNA

Chain H

50S RIBOSOMAL PROTEIN L10E

Chain W

50S ribosomal protein L30P