J4_6Y4B_001

3D structure

PDB id

6Y4B (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of cyclodipeptide synthase from Candidatus Glomeribacter gigasporarum bound to Phe-tRNAPhe

Experimental method

X-RAY DIFFRACTION

Resolution

5 Å

Loop

Sequence

A(4SU)AG*CAG*CGUGUCC*GU

Length

16 nucleotides

Bulged bases

6Y4B|1|F|4SU|8, 6Y4B|1|F|U|45, 6Y4B|1|F|U|47, 6Y4B|1|F|C|48

QA status

Modified nucleotides: 4SU

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

J4_6Y4B_001 not in the Motif Atlas

Homologous match to J4_3WFS_001

Geometric discrepancy: 0.3099

The information below is about J4_3WFS_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_36296.3

Basepair signature

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

Number of instances in this motif group

5

Unit IDs

6Y4B|1|F|A|7
6Y4B|1|F|4SU|8
6Y4B|1|F|A|9
6Y4B|1|F|G|10
*
6Y4B|1|F|C|25
6Y4B|1|F|A|26
6Y4B|1|F|G|27
*
6Y4B|1|F|C|43
6Y4B|1|F|G|44
6Y4B|1|F|U|45
6Y4B|1|F|G|46
6Y4B|1|F|U|47
6Y4B|1|F|C|48
6Y4B|1|F|C|49
*
6Y4B|1|F|G|65
6Y4B|1|F|U|66

Current chains

Chain F

RNA (77-MER)

Nearby chains

Chain A

Cyclodipeptide synthase