IL_1VY6_267

3D structure

PDB id

1VY6 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site.

Experimental method

X-RAY DIFFRACTION

Resolution

2.9 Å

Loop

Sequence

GGUAAAG*CGAAAAUGAUCGGGGC

Length

23 nucleotides

Bulged bases

1VY6|1|DA|U|1026, 1VY6|1|DA|A|1127, 1VY6|1|DA|U|1130

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_1VY6_267 not in the Motif Atlas

Geometric match to IL_7RQB_040

Geometric discrepancy: 0.0678

The information below is about IL_7RQB_040

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_50715.1

Basepair signature

cWW-tSH-tHH-L-R-L-R-L-tWW-L-cWW-L-L-L-R-L

Number of instances in this motif group

4

Unit IDs

1VY6|1|DA|G|1024
1VY6|1|DA|G|1025
1VY6|1|DA|U|1026
1VY6|1|DA|A|1027
1VY6|1|DA|A|1028
1VY6|1|DA|A|1029
1VY6|1|DA|G|1030
*
1VY6|1|DA|C|1124
1VY6|1|DA|G|1125
1VY6|1|DA|A|1126
1VY6|1|DA|A|1127
1VY6|1|DA|A|1128
1VY6|1|DA|A|1129
1VY6|1|DA|U|1130
1VY6|1|DA|G|1131
1VY6|1|DA|A|1132
1VY6|1|DA|U|1133
1VY6|1|DA|C|1135
1VY6|1|DA|G|1136
1VY6|1|DA|G|1137
1VY6|1|DA|G|1138
1VY6|1|DA|G|1139
1VY6|1|DA|C|1140

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain D9

50S ribosomal protein L36

Chain DB

5S ribosomal RNA; 5S rRNA

Chain DE

50S ribosomal protein L3

Chain DN

50S ribosomal protein L13

Chain DQ

50S ribosomal protein L16