J5_9B00_015

3D structure

PDB id

9B00 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with berberine analog of chloramphenicol CAM-BER, mRNA, deacylated A- and E-site tRNAphe, and deacylated P-site tRNAmet at 2.80A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

GCAAGUUGG*UG*CC*GUGAACAGG*CGC

Length

25 nucleotides

Bulged bases

9B00|1|2A|G|1758, 9B00|1|2A|G|1763

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

J5_9B00_015 not in the Motif Atlas

Homologous match to J5_9DFE_005

Geometric discrepancy: 0.0627

The information below is about J5_9DFE_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_99177.1

Basepair signature

cWW-F-F-F-cWW-F-F-F-F-F-F-F-F-F-cWW-F-cWW-cWW

Number of instances in this motif group

10

Unit IDs

9B00|1|2A|G|1674
9B00|1|2A|C|1675
9B00|1|2A|A|1676
9B00|1|2A|A|1677
9B00|1|2A|G|1678
9B00|1|2A|U|1679
9B00|1|2A|U|1680
9B00|1|2A|G|1681
9B00|1|2A|G|1682
*
9B00|1|2A|U|1706
9B00|1|2A|G|1707
*
9B00|1|2A|C|1751
9B00|1|2A|C|1752
*
9B00|1|2A|G|1756
9B00|1|2A|U|1757
9B00|1|2A|G|1758
9B00|1|2A|A|1759
9B00|1|2A|A|1760
9B00|1|2A|C|1761
9B00|1|2A|A|1762
9B00|1|2A|G|1763
9B00|1|2A|G|1764
*
9B00|1|2A|C|1988
9B00|1|2A|G|1989
9B00|1|2A|C|1990

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2E

50S ribosomal protein L3

Chain 2O

50S ribosomal protein L14

Chain 2T

50S ribosomal protein L19

Chain 2a

Small subunit ribosomal RNA; SSU rRNA