J4_4YVI_001

3D structure

PDB id

4YVI (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA

Experimental method

X-RAY DIFFRACTION

Resolution

3.01 Å

Loop

Sequence

GUCG*CG*UGGUG*CC

Length

13 nucleotides

Bulged bases

4YVI|1|C|U|8, 4YVI|1|C|U|48

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

J4_4YVI_001 not in the Motif Atlas

Homologous match to J4_5E6M_001

Geometric discrepancy: 0.1955

The information below is about J4_5E6M_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_35610.2

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW

Number of instances in this motif group

6

Unit IDs

4YVI|1|C|G|7
4YVI|1|C|U|8
4YVI|1|C|C|9
4YVI|1|C|G|10
*
4YVI|1|C|C|25
4YVI|1|C|G|26
*
4YVI|1|C|U|44
4YVI|1|C|G|45
4YVI|1|C|G|46
4YVI|1|C|U|48
4YVI|1|C|G|49
*
4YVI|1|C|C|65
4YVI|1|C|C|66

Current chains

Chain C

tRNA

Nearby chains

Chain A

tRNA (guanine-N(1)-)-methyltransferase

Chain B

tRNA (guanine-N(1)-)-methyltransferase