J3_5VP2_062

3D structure

PDB id

5VP2 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in complex with madumycin II and bound to mRNA and A-, P- and E-site tRNAs at 2.8A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

5VP2|1|2A|U|504, 5VP2|1|2A|G|508

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

J3_5VP2_062 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.057

The information below is about J3_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_17917.1

Basepair signature

cWW-tWH-cSS-cWW-tSH-tHH-cWW-F-F-tWW-tSS-cSS-tWW-tSH-tWH-cSW-F-tHS-cWW-F

Number of instances in this motif group

9

Unit IDs

5VP2|1|2A|G|30
5VP2|1|2A|C|31
*
5VP2|1|2A|G|474
5VP2|1|2A|U|475
5VP2|1|2A|G|476
5VP2|1|2A|A|477
5VP2|1|2A|A|478
5VP2|1|2A|A|479
5VP2|1|2A|A|480
5VP2|1|2A|G|481
5VP2|1|2A|A|482
5VP2|1|2A|A|483
5VP2|1|2A|C|484
*
5VP2|1|2A|G|496
5VP2|1|2A|A|497
5VP2|1|2A|G|498
5VP2|1|2A|U|499
5VP2|1|2A|G|500
5VP2|1|2A|A|501
5VP2|1|2A|A|502
5VP2|1|2A|A|503
5VP2|1|2A|U|504
5VP2|1|2A|A|505
5VP2|1|2A|G|506
5VP2|1|2A|A|507
5VP2|1|2A|G|508
5VP2|1|2A|C|509
5VP2|1|2A|C|510

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2U

50S ribosomal protein L20

Chain 2W

50S ribosomal protein L22

Chain 2Y

50S ribosomal protein L24