J5_5NDK_003

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

CGAUGAAG*CGAAUG*CG*CAC*GGG

Length

22 nucleotides

Bulged bases

5NDK|1|14|U|49

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_5NDK_003 not in the Motif Atlas

Homologous match to J5_9DFE_001

Geometric discrepancy: 0.0525

The information below is about J5_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_27223.1

Basepair signature

cWW-cWW-cWW-cWW-F-cWW-F-tSH-F-tHH-tHS-cWW

Number of instances in this motif group

7

Unit IDs

5NDK|1|14|C|46
5NDK|1|14|G|47
5NDK|1|14|A|48
5NDK|1|14|U|49
5NDK|1|14|G|50
5NDK|1|14|A|51
5NDK|1|14|A|52
5NDK|1|14|G|53
*
5NDK|1|14|C|114
5NDK|1|14|G|115
5NDK|1|14|A|116
5NDK|1|14|A|117
5NDK|1|14|U|118
5NDK|1|14|G|119
*
5NDK|1|14|C|128
5NDK|1|14|G|129
*
5NDK|1|14|C|148
5NDK|1|14|A|149
5NDK|1|14|C|150
*
5NDK|1|14|G|166
5NDK|1|14|G|167
5NDK|1|14|G|168

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain B5

50S ribosomal protein L23

Chain L5

50S ribosomal protein L34