SMTL ID : 8p2s.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 14 residues within 4Å: Chain A: S.195, R.196, P.197, K.199, R.200, T.203, V.206, L.207 Chain B: Q.294, E.297, A.298, H.301, N.302 Ligands: MG.3 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.195, A:R.196, A:R.196, A:K.199, A:T.203, B:N.302, B:N.302 Salt bridges: A:R.196, A:K.199, A:R.200, A:R.200 Hydrophobic interactions: B:A.298 TTP.4: 16 residues within 4Å: Chain A: Q.294, E.297, A.298, H.301, N.302 Chain B: S.195, R.196, P.197, A.198, K.199, R.200, T.203, V.206, L.207, I.210 Ligands: MG.2 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.196, B:R.196, B:K.199, B:T.203, A:E.297, A:N.302, A:N.302 Salt bridges: B:R.196, B:K.199, B:R.200, B:R.200, B:R.200 Hydrophobic interactions: A:A.298, A:H.301

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.294, E.297 Chain B: R.200 Ligands: TTP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.297 MG.3: 4 residues within 4Å: Chain A: R.200 Chain B: Q.294, E.297 Ligands: TTP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.297

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.5: 23 residues within 4Å: Chain B: E.117, N.118, N.120, H.161, H.163, D.164, T.174, Q.216, H.220, G.221, G.222, Q.313, V.314, F.316, C.420, T.422, F.442, P.583, A.584, E.585, G.586, L.587, Y.716 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:E.117, B:N.118, B:N.120, B:D.164, B:Q.216, B:G.222, B:Q.313, B:V.314, B:V.314, B:T.422, B:T.422, B:E.585, B:E.585, B:G.586, B:L.587 Salt bridges: B:H.161, B:H.161, 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. eLife (2023)

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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