SMTL ID : 9bx2.1

Class 2 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x TTP: THYMIDINE-5'-TRIPHOSPHATE

TTP.1: 14 residues within 4Å: Chain A: D.177, S.178, L.179, I.182, L.206, R.207, I.213, K.214, T.220, K.221 Chain B: K.194, Y.236, A.237 Ligands: MG.2 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.179, A:I.182, A:I.213, B:K.194 Hydrogen bonds: A:D.177, A:L.179, A:K.214, A:K.221, B:Y.236 Salt bridges: A:R.207, A:R.207, A:K.214, A:K.214, A:H.304, B:K.194, B:K.194 TTP.4: 13 residues within 4Å: Chain A: K.194, Y.236, A.237 Chain B: D.177, S.178, L.179, I.182, R.207, I.213, K.214, T.220, K.221 Ligands: MG.5 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.179, B:I.182, B:I.213, A:K.194 Hydrogen bonds: B:D.177, B:L.179, B:K.214, B:K.221, A:Y.236 Salt bridges: B:R.207, B:R.207, B:K.214, B:K.214, A:K.194, A:K.194

2 x MG: MAGNESIUM ION

MG.2: 1 residues within 4Å: Ligands: TTP.1 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: D.177, S.178, R.207 Ligands: TTP.4 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.3: 8 residues within 4Å: Chain A: K.30, V.33, H.34, F.37, N.42, F.89, R.90, F.91 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.30, A:N.42, A:R.90, A:F.91, A:F.91 Salt bridges: A:H.34, A:R.90 pi-Stacking: A:F.37, A:F.37 ATP.6: 9 residues within 4Å: Chain B: K.30, V.33, H.34, F.37, N.42, K.88, F.89, R.90, F.91 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.30, B:N.42, B:R.90, B:F.91, B:F.91 Salt bridges: B:H.34, B:K.88, B:R.90 pi-Stacking: B:F.37, B:F.37

4 x MN: MANGANESE (II) ION

MN.7: 5 residues within 4Å: Chain C: E.118, E.185, E.219, H.222 Ligands: MN.8 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.118, C:E.185, C:E.185, C:E.219, C:H.222 MN.8: 6 residues within 4Å: Chain C: D.87, E.118, H.122, F.189, E.219 Ligands: MN.7 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.87, C:E.118, C:H.122, C:E.219, C:E.219 MN.9: 5 residues within 4Å: Chain D: E.118, E.185, E.219, H.222 Ligands: MN.10 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.118, D:E.185, D:E.185, D:E.219, D:H.222 MN.10: 5 residues within 4Å: Chain D: D.87, E.118, H.122, E.219 Ligands: MN.9 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.87, D:D.87, D:E.118, D:H.122, D:E.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, D. et al., Conformational landscapes of a class I ribonucleotide reductase complex during turnover reveal intrinsic dynamics and asymmetry. Nat Commun (2025)

Release Date

2025-03-19

Peptides

Ribonucleoside-diphosphate reductase subunit alpha: AB
Ribonucleoside-diphosphate reductase subunit beta: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ribonucleoside-diphosphate reductase subunit alpha

Ribonucleoside-diphosphate reductase subunit beta

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