SMTL ID : 9fzf.2 (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-tetramer

Ligands

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

DTP.1: 14 residues within 4Å: Chain A: K.53, K.65, G.69, R.72, A.73, R.126, F.127, V.130, Y.131 Chain D: R.72, E.75 Ligands: ADP.2, MG.4, DTP.13 9 PLIP interactions: 1 interactions with chain D, 8 interactions with chain A Hydrogen bonds: D:R.72, A:R.72 Hydrophobic interactions: A:F.127, A:V.130 Water bridges: A:G.69 Salt bridges: A:K.53, A:K.53, A:K.65, A:K.65 DTP.5: 14 residues within 4Å: Chain B: K.53, K.65, G.69, R.72, A.73, R.126, F.127, V.130, Y.131 Chain C: R.72, E.75 Ligands: ADP.6, MG.8, DTP.9 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.127, B:V.130 Hydrogen bonds: B:R.72, C:R.72 Water bridges: B:G.69 Salt bridges: B:K.53, B:K.53, B:K.65, B:K.65 DTP.9: 14 residues within 4Å: Chain B: R.72, E.75 Chain C: K.53, K.65, G.69, R.72, A.73, R.126, F.127, V.130, Y.131 Ligands: DTP.5, ADP.10, MG.12 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.127, C:V.130 Hydrogen bonds: C:R.72, B:R.72 Water bridges: C:G.69 Salt bridges: C:K.53, C:K.53, C:K.65, C:K.65 DTP.13: 14 residues within 4Å: Chain A: R.72, E.75 Chain D: K.53, K.65, G.69, R.72, A.73, R.126, F.127, V.130, Y.131 Ligands: DTP.1, ADP.14, MG.16 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.127, D:V.130 Hydrogen bonds: D:R.72, A:R.72 Water bridges: D:G.69 Salt bridges: D:K.53, D:K.53, D:K.65, D:K.65

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.2: 17 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 Ligands: DTP.1, MG.4 12 PLIP interactions: 1 interactions with chain D, 11 interactions with chain A Salt bridges: D:K.76, A:K.53 Hydrogen bonds: A:K.53, A:S.54, A:P.60, A:N.62, A:S.105 Water bridges: A:S.54, A:S.54, A:K.65, A:G.69, A:G.69 ADP.6: 17 residues within 4Å: 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 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.53, B:S.54, B:P.60, B:N.62, B:S.105 Water bridges: B:S.54, B:S.54, B:K.65, B:G.69, B:G.69 Salt bridges: B:K.53, C:K.76 ADP.10: 17 residues within 4Å: Chain C: 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.9, MG.12 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.53, C:S.54, C:E.59, C:P.60, C:N.62, C:S.105 Water bridges: C:S.54, C:S.54, C:K.65, C:G.69, C:G.69 Salt bridges: C:K.53, B:K.76 ADP.14: 17 residues within 4Å: Chain D: 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.13, MG.16 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.53, D:S.54, D:E.59, D:P.60, D:N.62, D:S.105 Water bridges: D:S.54, D:S.54, D:K.65, D:G.69, D:G.69 Salt bridges: D:K.53, A:K.76

4 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 ZN.11: 4 residues within 4Å: Chain C: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.3, C:C.6, C:C.31, C:C.34 ZN.15: 4 residues within 4Å: Chain D: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.3, D:C.6, D:C.31, D:C.34

4 x MG: MAGNESIUM ION

MG.4: 2 residues within 4Å: Ligands: DTP.1, ADP.2 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Ligands: DTP.5, ADP.6 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Ligands: DTP.9, ADP.10 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Ligands: DTP.13, ADP.14 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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Transcriptional repressor NrdR

Related Entries With Identical Sequence