HL_1KD1_061

3D structure

PDB id

1KD1 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui

Experimental method

X-RAY DIFFRACTION

Resolution

3 Å

Loop

Sequence

GCUUGAUGC

Length

9 nucleotides

Bulged bases

1KD1|1|A|C|2443

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

HL_1KD1_061 not in the Motif Atlas

Homologous match to HL_4V9F_061

Geometric discrepancy: 0.0378

The information below is about HL_4V9F_061

Detailed Annotation

Pseudoknot geometry

Broad Annotation

No text annotation

Motif group

HL_52651.2

Basepair signature

cWW-F-F-F-F-F-F

Number of instances in this motif group

29

Unit IDs

1KD1|1|A|G|2442
1KD1|1|A|C|2443
1KD1|1|A|U|2444
1KD1|1|A|U|2445
1KD1|1|A|G|2446
1KD1|1|A|A|2447
1KD1|1|A|U|2448
1KD1|1|A|G|2449
1KD1|1|A|C|2450

Current chains

Chain A

23S RRNA

Nearby chains

Chain 4

RIBOSOMAL PROTEIN L44E

Chain M

RIBOSOMAL PROTEIN L15

Chain N

RIBOSOMAL PROTEIN L15E