SMTL ID : 7pq9.4 (6 other biounits)

Crystal structure of Bacillus clausii pdxR at 2.8 Angstroms resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: C.167, T.168 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 2 residues within 4Å: Chain A: H.328, N.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.328, A:N.332

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 4 residues within 4Å: Chain A: A.176, T.340, V.341 Chain B: T.340 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:T.340, B:T.340, H2O.1, H2O.1 CA.4: 3 residues within 4Å: Chain A: L.209, Y.212, N.214 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.209, A:Y.212, A:N.214 CA.5: 3 residues within 4Å: Chain A: G.391, S.394, H.397 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:G.391, A:S.394, A:H.397 CA.6: 4 residues within 4Å: Chain B: L.209, Y.212, N.214, D.215 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:L.209, B:Y.212, B:N.214 CA.7: 6 residues within 4Å: Chain B: P.248, I.390, G.391, S.394, H.397, I.398 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.391, B:H.397 CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.9: 5 residues within 4Å: Chain B: E.154, Y.157, H.161, M.353, K.354 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freda, I. et al., Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR. Nucleic Acids Res. (2023)

Release Date

2022-09-28

Peptides

PLP-dependent aminotransferase family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
GGG

B
HHH

PLP-dependent aminotransferase family protein

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