SMTL ID : 8p23.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

ATP.1: 10 residues within 4Å: Chain A: K.23, K.30, A.31, H.34, K.83, Y.84, Y.87, R.91 Chain B: R.15 Ligands: ATP.2 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.30, A:H.34, A:Y.84 Salt bridges: A:K.30, A:R.91, B:R.15 pi-Stacking: A:Y.87, A:Y.87 ATP.2: 12 residues within 4Å: Chain A: K.11, R.12, D.13, F.19, K.23, I.24, V.61, Y.84, R.88, R.91 Chain B: R.95 Ligands: ATP.1 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.12, A:D.13, A:Y.84, A:Y.84, B:R.95 Salt bridges: A:R.12, A:R.88, A:R.88, A:R.91 ATP.4: 10 residues within 4Å: Chain A: R.15 Chain B: K.11, K.23, A.27, K.30, K.83, Y.84, Y.87, R.91 Ligands: ATP.5 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.84, B:R.88, A:R.15 Salt bridges: B:K.11, B:K.23, B:K.23, B:R.91, A:R.15 pi-Stacking: B:Y.87, B:Y.87 ATP.5: 15 residues within 4Å: Chain A: R.95 Chain B: V.9, K.11, R.12, V.17, G.18, F.19, K.23, I.24, A.27, V.61, Y.84, R.88, R.91 Ligands: ATP.4 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.18, B:N.20, B:Y.84, B:Y.84, B:R.91, A:R.95 Salt bridges: B:R.12, B:R.12, B:R.88, B:R.91

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.3: 16 residues within 4Å: Chain B: E.117, N.118, N.120, H.163, H.220, G.221, Q.313, F.316, C.420, F.442, T.582, P.583, A.584, E.585, G.586, L.587 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.316 Hydrogen bonds: B:N.120, B:Q.313, B:P.583, B:E.585, B:E.585, B:E.585, B:G.586, B:L.587 Salt bridges: B:H.163, B:H.163

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain B: C.687, C.699, K.701, C.702 3 PLIP interactions: 3 interactions with chain B Metal complexes: 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

2023-08-30

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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