SMTL ID : 7p3f.1

Streptomyces coelicolor dATP/ATP-loaded NrdR in complex with its cognate DNA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 13 residues within 4Å: Chain A: K.50, R.51, E.56, P.57, F.58, S.59, K.62, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.50, A:R.51, A:P.57, A:S.59, A:K.62 Salt bridges: A:K.50, A:R.51 ATP.4: 13 residues within 4Å: Chain B: K.50, R.51, E.56, P.57, F.58, S.59, K.62, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.50, B:R.51, B:P.57, B:S.59, B:K.62 Salt bridges: B:K.50, B:R.51 ATP.7: 15 residues within 4Å: Chain C: V.48, K.50, R.51, E.56, P.57, F.58, S.59, K.62, V.63, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.50, C:R.51, C:P.57, C:S.59, C:T.102 Salt bridges: C:K.50, C:K.50, C:R.51, C:R.51, C:R.51 ATP.10: 15 residues within 4Å: Chain D: V.48, K.50, R.51, E.56, P.57, F.58, S.59, K.62, V.63, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.11 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.50, D:R.51, D:P.57, D:S.59, D:T.102 Salt bridges: D:K.50, D:K.50, D:R.51, D:R.51, D:R.51

4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.2: 12 residues within 4Å: Chain A: K.50, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Chain C: Q.72 Ligands: ATP.1, DTP.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.127 Salt bridges: A:K.50, A:K.62, A:K.62, A:K.69 DTP.5: 12 residues within 4Å: Chain B: K.50, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Chain D: Q.72 Ligands: ATP.4, DTP.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.127 Salt bridges: B:K.50, B:K.62, B:K.62, B:K.69 DTP.8: 13 residues within 4Å: Chain A: K.69, Q.72 Chain C: K.50, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Ligands: DTP.2, ATP.7 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.127 Salt bridges: C:K.50, C:K.62, C:K.69 Hydrogen bonds: A:K.69 DTP.11: 13 residues within 4Å: Chain B: K.69, Q.72 Chain D: K.50, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Ligands: DTP.5, ATP.10 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.127 Salt bridges: D:K.50, D:K.62, D:K.69

4 x ZN: ZINC ION(Non-covalent)

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.6: 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.9: 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.12: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rozman Grinberg, I. et al., A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases. Nat Commun (2022)

Release Date

2022-05-11

Peptides

Transcriptional repressor NrdR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Transcriptional repressor NrdR

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