IL_5DM8_039

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

GAGUG*CUC

Length

8 nucleotides

Bulged bases

5DM8|1|X|A|1088

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_039 not in the Motif Atlas

Geometric match to IL_7RQB_022

Geometric discrepancy: 0.2983

The information below is about IL_7RQB_022

Detailed Annotation

Major groove platform with extra cWW

Broad Annotation

Major groove platform

Motif group

IL_05564.2

Basepair signature

cWW-cSH-cWW-cWW

Number of instances in this motif group

14

Unit IDs

5DM8|1|X|G|1087
5DM8|1|X|A|1088
5DM8|1|X|G|1089
5DM8|1|X|U|1090
5DM8|1|X|G|1091
*
5DM8|1|X|C|1100
5DM8|1|X|U|1101
5DM8|1|X|C|1102

Current chains

Chain X

Deinococcus radiodurans R1 chromosome 1, complete sequence

Nearby chains

Chain E

50S ribosomal protein L6

Chain F

50S ribosomal protein L11