SMTL ID : 8vhu.1

Crystal structure of dATP bound E. coli class Ia ribonucleotide reductase alpha construct fused with the C-terminal tail of E. coli class Ia beta subunit

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

DTP.1: 16 residues within 4Å: Chain A: V.26, K.28, R.29, E.34, R.35, I.36, N.37, K.40, I.41, V.44, T.74, H.78, I.81, F.106, K.110 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.29, A:E.34, A:N.37, A:H.78 Water bridges: A:K.28, A:K.28, A:K.28, A:K.28, A:D.30, A:K.110, A:K.110, A:K.110, A:K.110 Salt bridges: A:K.28, A:K.28, A:R.29, A:R.29, A:K.110, A:K.110, A:K.110 DTP.3: 13 residues within 4Å: Chain A: D.251, S.252, L.253, I.280, R.281, I.287, R.288, F.293, H.294, T.295 Chain B: S.268, C.311 Ligands: MG.4 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.253 Hydrogen bonds: A:D.251, A:L.253, A:R.288, A:T.295 Water bridges: A:D.254, A:R.281, A:R.281, A:R.288, A:G.289, B:S.268 Salt bridges: A:R.281, A:R.288 DTP.9: 13 residues within 4Å: Chain A: S.268, C.311 Chain B: D.251, S.252, L.253, I.256, I.280, R.281, I.287, R.288, H.294, T.295 Ligands: MG.10 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.253, B:I.256 Hydrogen bonds: B:D.251, B:L.253, B:R.288, A:S.268 Water bridges: B:R.281, B:R.281 Salt bridges: B:R.281, B:R.288

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: K.28 Ligands: DTP.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: DTP.3 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: DTP.9 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain A: N.257, S.260, S.261 Chain B: N.257, S.260, S.261 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.257, B:S.261 Water bridges: A:S.260, B:S.260

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: Q.305, R.348, V.349, R.350, H.351 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: S.641, E.642, T.643, S.644 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: K.603, K.604 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: Q.305, R.348, V.349, R.350 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: S.641, E.642, T.643, S.644 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: K.603, K.604 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 3 residues within 4Å: Chain B: Q.210, Y.211, R.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.210, B:R.214, B:R.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Funk, M.A. et al., How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase. Biochemistry (2024)

Release Date

2024-09-04

Peptides

Fusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta