SMTL ID : 8bt1.1

YdaT transcription regulator (CII functional analog)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: R.128, V.132 Chain C: R.128, V.132 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.128, A:R.128, C:R.128, C:R.128 GOL.4: 3 residues within 4Å: Chain C: F.54, D.65, D.66 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.66, C:D.66

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 1 residues within 4Å: Chain A: R.130 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain C: H.68 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain B: Y.64, R.74, K.78 4 PLIP interactions: 4 interactions with chain B Water bridges: B:Y.64, B:R.74 Salt bridges: B:R.74, B:K.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prolic-Kalinsek, M. et al., Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7. Acta Crystallogr D Struct Biol (2023)

Release Date

2023-02-22

Peptides

YdaT_toxin domain-containing protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

YdaT_toxin domain-containing protein