SMTL ID : 8uiw.1 (1 other biounit)

yjdF riboswitch from R. gauvreauii in complex with chelerythrine bound to Fab BL3-6 S97N

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: C.59, A.94, U.96 No protein-ligand interaction detected (PLIP)

1 x CTI: 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium(Non-functional Binders)

CTI.2: 7 residues within 4Å: Chain A: A.14, A.15, U.51, U.55, A.56, U.96, U.116 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-functional Binders)

K.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x OS: OSMIUM ION(Non-covalent)

OS.4: 1 residues within 4Å: Chain C: H.190 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.190 OS.5: 2 residues within 4Å: Chain C: S.1, D.2 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.1, C:D.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krochmal, D. et al., Structural basis for promiscuity in ligand recognition by yjdF riboswitch. Cell Discov (2024)

Release Date

2024-04-10

Peptides

Fab BL3-6 S97N heavy chain: B
Fab BL3-6 S97N light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
H

C
L

Fab BL3-6 S97N heavy chain

Fab BL3-6 S97N light chain

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