SMTL ID : 8p39.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 14 residues within 4Å: Chain A: R.196, P.197, A.198, K.199, R.200, T.203, V.206, I.210 Chain B: Q.294, A.298, H.301, N.302, T.305 Ligands: MG.3 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.196, A:K.199, A:R.200, A:T.203, B:N.302, B:N.302 Salt bridges: A:R.196 DGT.4: 14 residues within 4Å: Chain A: Q.294, E.297, A.298, H.301, N.302, T.305 Chain B: R.196, P.197, K.199, R.200, T.203, V.206, I.210 Ligands: MG.2 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.196, B:R.196, B:K.199, B:T.203, A:Q.294, A:N.302, A:N.302, A:N.302 Salt bridges: B:R.196, B:R.200

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: Q.294 Ligands: DGT.4 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain B: Q.294 Ligands: DGT.1 No protein-ligand interaction detected (PLIP)

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

ATP.5: 16 residues within 4Å: Chain B: E.117, N.118, N.120, H.161, H.163, D.164, H.220, G.221, Q.313, V.314, C.420, T.582, P.583, E.585, G.586, L.587 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.118, B:N.120, B:D.164, B:D.164, B:Q.313, B:V.314, B:P.583, B:E.585, B:G.586, B:L.587 Salt bridges: B:H.163, B:H.163, B:H.163

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain B: C.684, C.687, C.699, C.702 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.684, B:C.687, B:C.699, B:C.702

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bimai, O. et al., Activity modulation in anaerobic ribonucleotide reductase: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site. To be published

Release Date

2023-09-13

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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