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

Transcription repressor NrdR from E. coli, AMPPNP/ATP-bound state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-tetramer

Ligands

4 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: ANP.2, MG.4, DTP.5 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.127, A:V.130 Hydrogen bonds: A:R.72, B:R.72 Water bridges: A:V.130, B:K.76, 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, ANP.6, MG.8 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.127, B:V.130 Hydrogen bonds: B:R.72, A:R.72 Water bridges: B:K.53, B:K.65, A:E.75, A:E.75 Salt bridges: B:K.53, B:K.53, B:K.65, B:K.65, A:K.76 DTP.9: 15 residues within 4Å: Chain C: K.53, K.65, G.69, R.72, A.73, R.126, F.127, V.130, Y.131 Chain D: R.72, E.75, K.76 Ligands: ANP.10, MG.12, DTP.13 13 PLIP interactions: 4 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:R.72, D:K.76, C:R.72 Water bridges: D:E.75, C:K.53, C:K.53 Salt bridges: D:K.76, C:K.53, C:K.53, C:K.65, C:K.65 Hydrophobic interactions: C:F.127, C:V.130 DTP.13: 15 residues within 4Å: Chain C: R.72, E.75, K.76 Chain D: K.53, K.65, G.69, R.72, A.73, R.126, F.127, V.130, Y.131 Ligands: DTP.9, ANP.14, MG.16 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:F.127, D:V.130 Hydrogen bonds: D:R.72, C:R.72 Water bridges: D:K.53, D:K.53, D:V.130, C:K.76, C:K.76, C:K.76 Salt bridges: D:K.53, D:K.53, D:K.65, D:K.65, C:K.76

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

ANP.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 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.53, A:K.53, A:S.54, A:S.54, A:S.54, A:E.59, A:P.60, A:N.62, A:S.105, B:K.76 ANP.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 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.53, B:S.54, B:S.54, B:P.60, B:N.62, B:S.105, A:K.76 Water bridges: B:N.55, B:K.65, B:G.69 Salt bridges: A:K.76 ANP.10: 18 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 Chain D: K.76 Ligands: DTP.9, MG.12 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.53, C:S.54, C:S.54, C:E.59, C:P.60, C:N.62, C:S.105, D:K.76 Water bridges: C:N.55, C:Y.131, D:K.76 Salt bridges: D:K.76 ANP.14: 18 residues within 4Å: Chain C: K.76 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 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.53, D:S.54, D:S.54, D:P.60, D:N.62, D:S.105, C:K.76, C:K.76, C:K.76 Water bridges: D:S.54, D:S.54

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, ANP.2 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: K.53 Ligands: DTP.5, ANP.6 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: K.53 Ligands: DTP.9, ANP.10 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain D: K.53 Ligands: DTP.13, ANP.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
A

B
B

C
C

D
D

Transcriptional repressor NrdR

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