J3_9D7S_003

3D structure

PDB id

9D7S (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with Api antimicrobial peptide, mRNA, A-site release factor 1, and deacylated P-site and E-site tRNAphe at 2.85A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.85 Å

Loop

Sequence

CUCG*CGAUAGCGCACCAGUAC*GGAAAG

Length

27 nucleotides

Bulged bases

9D7S|1|1A|U|448, 9D7S|1|1A|C|456

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_9D7S_003 not in the Motif Atlas

Homologous match to J3_9DFE_003

Geometric discrepancy: 0.0535

The information below is about J3_9DFE_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_30040.2

Basepair signature

cWW-tWH-F-cWW-tSS-tHH-cSS-tWH-tSW-tHS-cWW-tWH-F-cSH-tSS-F-F

Number of instances in this motif group

7

Unit IDs

9D7S|1|1A|C|32
9D7S|1|1A|U|33
9D7S|1|1A|C|34
9D7S|1|1A|G|35
*
9D7S|1|1A|C|445
9D7S|1|1A|G|446
9D7S|1|1A|A|447
9D7S|1|1A|U|448
9D7S|1|1A|A|449
9D7S|1|1A|G|450
9D7S|1|1A|C|451
9D7S|1|1A|G|452
9D7S|1|1A|C|453
9D7S|1|1A|A|454
9D7S|1|1A|C|455
9D7S|1|1A|C|456
9D7S|1|1A|A|457
9D7S|1|1A|G|458
9D7S|1|1A|U|459
9D7S|1|1A|A|460
9D7S|1|1A|C|461
*
9D7S|1|1A|G|468
9D7S|1|1A|G|469
9D7S|1|1A|A|470
9D7S|1|1A|A|471
9D7S|1|1A|A|472
9D7S|1|1A|G|473

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 17

50S ribosomal protein L34

Chain 1F

50S ribosomal protein L4

Chain 1U

50S ribosomal protein L20

Chain 1X

50S ribosomal protein L23