IL_5DOY_042

3D structure

PDB id

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

Description

Crystal structure of the Thermus thermophilus 70S ribosome in complex with antibiotic Hygromycin A, mRNA and three tRNAs in the A, P and E sites at 2.6A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.6 Å

Loop

Sequence

GAGUG*CUC

Length

8 nucleotides

Bulged bases

5DOY|1|1A|A|1088

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_5DOY_042 not in the Motif Atlas

Geometric match to IL_1MMS_002

Geometric discrepancy: 0.1893

The information below is about IL_1MMS_002

Detailed Annotation

Major groove platform with extra cWW

Broad Annotation

Major groove platform

Motif group

IL_51387.3

Basepair signature

cWW-cSH-cWW-cWW

Number of instances in this motif group

21

Unit IDs

5DOY|1|1A|G|1087
5DOY|1|1A|A|1088
5DOY|1|1A|G|1089
5DOY|1|1A|U|1090
5DOY|1|1A|G|1091
*
5DOY|1|1A|C|1100
5DOY|1|1A|U|1101
5DOY|1|1A|C|1102

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 19

50S Ribosomal Protein L36