3D structure

PDB id
5MDY (explore in PDB, NAKB, or RNA 3D Hub)
Description
Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state)
Experimental method
ELECTRON MICROSCOPY
Resolution
3.35 Å

Loop

Sequence
UUUA*UUUG*CU*AG*CGGAUAAAA
Length
21 nucleotides
Bulged bases
5MDY|1|1|U|2076, 5MDY|1|1|G|2428, 5MDY|1|1|G|2429, 5MDY|1|1|A|2430, 5MDY|1|1|U|2431
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_5MDY_006 not in the Motif Atlas
Homologous match to J5_4WF9_007
Geometric discrepancy: 0.1154
The information below is about J5_4WF9_007
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
J5_39529.2
Basepair signature
cWW-cWH-cWH-F-cWW-F-F-cWW-F-cWW-cWW
Number of instances in this motif group
4

Unit IDs

5MDY|1|1|U|2074
5MDY|1|1|U|2075
5MDY|1|1|U|2076
5MDY|1|1|A|2077
*
5MDY|1|1|U|2243
5MDY|1|1|U|2244
5MDY|1|1|U|2245
5MDY|1|1|G|2246
*
5MDY|1|1|C|2258
5MDY|1|1|U|2259
*
5MDY|1|1|A|2281
5MDY|1|1|G|2282
*
5MDY|1|1|C|2427
5MDY|1|1|G|2428
5MDY|1|1|G|2429
5MDY|1|1|A|2430
5MDY|1|1|U|2431
5MDY|1|1|A|2432
5MDY|1|1|A|2433
5MDY|1|1|A|2434
5MDY|1|1|A|2435

Current chains

Chain 1
23S ribosomal RNA

Nearby chains

Chain B
50S ribosomal protein L2
Chain L
50S ribosomal protein L15
Chain W
50S ribosomal protein L27
Chain X
50S ribosomal protein L28
Chain c
50S ribosomal protein L33
Chain e
50S ribosomal protein L35

Coloring options:


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