3D structure

PDB id
5GAK (explore in PDB, NAKB, or RNA 3D Hub)
Description
Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A
Experimental method
ELECTRON MICROSCOPY
Resolution
3.88 Å

Loop

Sequence
UUGA*UUUG*CA*UG*CAGAAAA
Length
19 nucleotides
Bulged bases
5GAK|1|1|G|2418, 5GAK|1|1|U|2613, 5GAK|1|1|A|2799, 5GAK|1|1|G|2800, 5GAK|1|1|A|2801, 5GAK|1|1|A|2802, 5GAK|1|1|A|2803
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_5GAK_005 not in the Motif Atlas
Homologous match to J5_8P9A_015
Geometric discrepancy: 0.2245
The information below is about J5_8P9A_015
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
J5_08912.1
Basepair signature
cWW-cWH-cWH-tSS-cWW-cWW-cWW-F-cWW
Number of instances in this motif group
3

Unit IDs

5GAK|1|1|U|2416
5GAK|1|1|U|2417
5GAK|1|1|G|2418
5GAK|1|1|A|2419
*
5GAK|1|1|U|2611
5GAK|1|1|U|2612
5GAK|1|1|U|2613
5GAK|1|1|G|2614
*
5GAK|1|1|C|2627
5GAK|1|1|A|2628
*
5GAK|1|1|U|2650
5GAK|1|1|G|2651
*
5GAK|1|1|C|2798
5GAK|1|1|A|2799
5GAK|1|1|G|2800
5GAK|1|1|A|2801
5GAK|1|1|A|2802
5GAK|1|1|A|2803
5GAK|1|1|A|2804

Current chains

Chain 1
25S rRNA

Nearby chains

Chain C
60S ribosomal protein L42-A
Chain E
60S ribosomal protein L2-A
Chain P
60S ribosomal protein L15-A
Chain S
60S ribosomal protein L18-A
Chain V
60S ribosomal protein L21-A
Chain c
60S ribosomal protein L28
Chain d
60S ribosomal protein L29
Chain q
Eukaryotic translation initiation factor 5A-1

Coloring options:


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