IL_5DM8_027

3D structure

PDB id

5DM8 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with orthoformimycin

Experimental method

X-RAY DIFFRACTION

Resolution

3.1 Å

Loop

Sequence

GCACU*AAAC

Length

9 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

IL_5DM8_027 not in the Motif Atlas

Geometric match to IL_4WF9_033

Geometric discrepancy: 0.1069

The information below is about IL_4WF9_033

Detailed Annotation

C-loop

Broad Annotation

No text annotation

Motif group

IL_16301.2

Basepair signature

cWW-cWS-tWH-R-L-R-cWW

Number of instances in this motif group

10

Unit IDs

5DM8|1|X|G|864
5DM8|1|X|C|865
5DM8|1|X|A|866
5DM8|1|X|C|867
5DM8|1|X|U|868
*
5DM8|1|X|A|909
5DM8|1|X|A|910
5DM8|1|X|A|911
5DM8|1|X|C|912

Current chains

Chain X

Deinococcus radiodurans R1 chromosome 1, complete sequence

Nearby chains

Chain J

50S ribosomal protein L16

Chain S

50S ribosomal protein L25

Chain Y

5S ribosomal RNA; 5S rRNA