SMTL ID : 8p27.1

Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its dimeric, dATP-bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

DTP.1: 13 residues within 4Å: Chain A: S.195, R.196, P.197, K.199, R.200, T.203, V.206 Chain B: Q.294, E.297, A.298, H.301, N.302 Ligands: MG.4 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:Q.294, B:N.302, A:S.195, A:R.196, A:R.196, A:K.199, A:T.203 Salt bridges: A:R.196, A:R.200, A:R.200 DTP.3: 13 residues within 4Å: Chain A: Q.294, E.297, A.298, H.301, N.302 Chain B: S.195, R.196, P.197, K.199, R.200, T.203, V.206 Ligands: MG.2 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.195, B:R.196, B:R.196, B:K.199, B:T.203, A:Q.294, A:N.302 Salt bridges: B:R.196, B:R.200, B:R.200

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.294, E.297 Ligands: DTP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.297 MG.4: 3 residues within 4Å: Chain B: Q.294, E.297 Ligands: DTP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bimai, O. et al., Activity modulation in anaerobic ribonucleotide reductases: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site. Elife (2023)

Release Date

2023-08-30

Peptides

Anaerobic ribonucleoside-triphosphate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Anaerobic ribonucleoside-triphosphate reductase

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