SMTL ID : 9fzf.1 (1 other biounit)

Transcriptional repressor NrdR from E. coli, ADP/dATP bound state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-dimer

Ligands

2 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

DTP.1: 15 residues within 4Å: Chain A: K.53, K.65, G.69, R.72, A.73, R.126, F.127, V.130, Y.131 Chain B: R.72, E.75, K.76 Ligands: ADP.2, MG.4, DTP.5 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.130 Hydrogen bonds: A:R.72, B:R.72, B:K.76, B:K.76 Salt bridges: A:K.53, A:K.53, A:K.65, A:K.65, B:K.76 DTP.5: 15 residues within 4Å: Chain A: R.72, E.75, K.76 Chain B: K.53, K.65, G.69, R.72, A.73, R.126, F.127, V.130, Y.131 Ligands: DTP.1, ADP.6, MG.8 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.130 Hydrogen bonds: B:R.72, A:R.72, A:K.76, A:K.76 Salt bridges: B:K.53, B:K.53, B:K.65, B:K.65, A:K.76

2 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.2: 18 residues within 4Å: Chain A: V.51, K.53, S.54, E.59, P.60, F.61, N.62, K.65, L.66, S.105, I.108, G.109, V.112, F.127, Y.131 Chain B: K.76 Ligands: DTP.1, MG.4 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.53, A:S.54, A:P.60, A:N.62, A:S.105 Salt bridges: A:K.53, B:K.76 ADP.6: 18 residues within 4Å: Chain A: K.76 Chain B: V.51, K.53, S.54, E.59, P.60, F.61, N.62, K.65, L.66, S.105, I.108, G.109, V.112, F.127, Y.131 Ligands: DTP.5, MG.8 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.53, B:S.54, B:E.59, B:P.60, B:N.62, B:S.105 Salt bridges: B:K.53, A:K.76

2 x ZN: ZINC ION

ZN.3: 4 residues within 4Å: Chain A: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.3, A:C.6, A:C.31, A:C.34 ZN.7: 4 residues within 4Å: Chain B: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.3, B:C.6, B:C.31, B:C.34

2 x MG: MAGNESIUM ION

MG.4: 3 residues within 4Å: Chain A: K.53 Ligands: DTP.1, ADP.2 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: K.53 Ligands: DTP.5, ADP.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rozman Grinberg, I. et al., Bacterial transcriptional repressor NrdR - a flexible multifactorial nucleotide sensor. Febs J. (2025)

Release Date

2025-03-19

Peptides

Transcriptional repressor NrdR: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transcriptional repressor NrdR

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