J4_5NDK_021

3D structure

PDB id

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

Description

Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA

Experimental method

X-RAY DIFFRACTION

Resolution

2.95 Å

Loop

Sequence

GGUUC*GGUUAG*CU*ACCCGUAC

Length

21 nucleotides

Bulged bases

5NDK|1|1H|U|1390

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

J4_5NDK_021 not in the Motif Atlas

Homologous match to J4_9DFE_004

Geometric discrepancy: 0.0618

The information below is about J4_9DFE_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_69051.6

Basepair signature

cWW-F-cWW-F-tHW-F-cWW-F-F-F-F-F-cWW-cWW

Number of instances in this motif group

7

Unit IDs

5NDK|1|1H|G|1359
5NDK|1|1H|G|1360
5NDK|1|1H|U|1361
5NDK|1|1H|U|1362
5NDK|1|1H|C|1363
*
5NDK|1|1H|G|1387
5NDK|1|1H|G|1388
5NDK|1|1H|U|1389
5NDK|1|1H|U|1390
5NDK|1|1H|A|1391
5NDK|1|1H|G|1392
*
5NDK|1|1H|C|1453
5NDK|1|1H|U|1454
*
5NDK|1|1H|A|1646
5NDK|1|1H|C|1647
5NDK|1|1H|C|1648
5NDK|1|1H|C|1649
5NDK|1|1H|G|1650
5NDK|1|1H|U|1651
5NDK|1|1H|A|1652
5NDK|1|1H|C|1653

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain F8

50S ribosomal protein L23

Chain P8

50S ribosomal protein L34