SMTL ID : 8vho.1

Crystal Structure of E. coli class Ia ribonucleotide reductase alpha subunit bound to dATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

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

DTP.1: 17 residues within 4Å: Chain A: V.7, K.9, R.10, E.15, R.16, I.17, N.18, K.21, I.22, V.25, T.55, I.58, H.59, I.62, F.87, K.91 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.25 Hydrogen bonds: A:K.9, A:K.9, A:R.10, A:N.18, A:H.59 Water bridges: A:K.91, A:K.91 Salt bridges: A:K.9, A:R.10, A:R.10, A:K.91, A:K.91 DTP.3: 11 residues within 4Å: Chain A: D.232, S.233, L.234, R.262, I.268, R.269, H.275, T.276 Chain B: S.249, C.292 Ligands: MG.4 11 PLIP interactions: 1 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:S.249, A:D.232, A:L.234, A:R.269 Hydrophobic interactions: A:L.234 Water bridges: A:S.233, A:D.235, A:R.262, A:R.262 Salt bridges: A:R.262, A:R.269 DTP.7: 17 residues within 4Å: Chain B: V.7, K.9, R.10, E.15, R.16, I.17, N.18, K.21, I.22, V.25, T.55, I.58, H.59, I.62, F.87, K.91 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.25 Hydrogen bonds: B:K.9, B:R.10, B:E.15, B:R.16, B:N.18, B:T.55, B:H.59 Salt bridges: B:K.9, B:R.10, B:K.91, B:K.91 DTP.9: 13 residues within 4Å: Chain A: S.249, C.292 Chain B: D.232, S.233, L.234, I.261, R.262, I.268, R.269, F.274, H.275, T.276 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.234 Hydrogen bonds: B:D.232, B:L.234, B:R.269 Water bridges: B:R.262, B:R.262, B:R.269 Salt bridges: B:R.262, B:R.269

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: 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.8: 1 residues within 4Å: Ligands: DTP.7 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: DTP.9 No protein-ligand interaction detected (PLIP)

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 7 residues within 4Å: Chain A: G.32, H.34, D.76, Y.79, R.83, M.141, T.142 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.76, A:R.83 MES.11: 7 residues within 4Å: Chain B: G.32, H.34, D.76, Y.79, R.83, M.141, T.142 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.83 Water bridges: B:Y.79, B:Y.79 Salt bridges: B:D.76

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: A.559, K.560, G.563, H.609 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.560, A:H.609 Water bridges: A:A.564, A:A.564, A:A.564 GOL.12: 3 residues within 4Å: Chain B: L.348, K.584, Y.722 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.584, B:K.584

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

Ribonucleoside-diphosphate reductase 1 subunit alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase 1 subunit alpha

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