J5_5NDK_010

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

CUGG*CUUG*CUGAAC*GGUAAUAG*CGAG

Length

26 nucleotides

Bulged bases

None detected

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_010 not in the Motif Atlas

Homologous match to J5_4LFB_001

Geometric discrepancy: 0.0841

The information below is about J5_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_70703.1

Basepair signature

cWW-F-tWH-F-F-cWW-cWW-cWH-cWH-cWW-tSH-tWH-tHW-tHS-cWW

Number of instances in this motif group

1

Unit IDs

5NDK|1|1G|C|682
5NDK|1|1G|U|683
5NDK|1|1G|G|684
5NDK|1|1G|G|685
*
5NDK|1|1G|C|1044
5NDK|1|1G|U|1045
5NDK|1|1G|U|1046
5NDK|1|1G|G|1047
*
5NDK|1|1G|C|1077
5NDK|1|1G|U|1078
5NDK|1|1G|G|1079
5NDK|1|1G|A|1080
5NDK|1|1G|A|1081
5NDK|1|1G|C|1082
*
5NDK|1|1G|G|1122
5NDK|1|1G|G|1123
5NDK|1|1G|U|1124
5NDK|1|1G|A|1125
5NDK|1|1G|A|1126
5NDK|1|1G|U|1127
5NDK|1|1G|A|1128
5NDK|1|1G|G|1129
*
5NDK|1|1G|C|1174
5NDK|1|1G|G|1175
5NDK|1|1G|A|1176
5NDK|1|1G|G|1177

Current chains

Chain 1G

16S ribosomal RNA

Nearby chains

Chain 32

30S ribosomal protein S4

Chain 3A

30S ribosomal protein S12