SMTL ID : 9bzo.1

Class 50 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.1: 8 residues within 4Å: Chain A: V.33, H.34, F.37, N.42, F.89, R.90, F.91, R.117 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.42, A:R.90, A:R.90, A:F.91, A:F.91 Salt bridges: A:H.34 pi-Stacking: A:H.34, A:F.37 ATP.7: 7 residues within 4Å: Chain B: V.33, H.34, F.37, N.42, F.89, R.90, F.91 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.42, B:R.90, B:F.91, B:F.91, B:R.117 Salt bridges: B:H.34, B:R.90 pi-Stacking: B:F.37, B:F.37 pi-Cation interactions: B:R.90

2 x GDP: GUANOSINE-5'-DIPHOSPHATE

GDP.2: 11 residues within 4Å: Chain A: F.47, F.48, H.49, N.50, L.51, K.54, K.78, F.81, K.82, Y.85, D.120 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:F.48, A:F.48, A:F.48, A:L.51, A:K.54, A:K.82, A:K.82 Salt bridges: A:K.78, A:K.78, A:K.82, A:K.82 GDP.8: 11 residues within 4Å: Chain B: F.47, F.48, H.49, N.50, L.51, K.54, K.78, F.81, K.82, Y.85, D.120 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.48, B:F.48, B:F.48, B:L.51, B:K.54 Salt bridges: B:K.78, B:K.78

2 x TTP: THYMIDINE-5'-TRIPHOSPHATE

TTP.3: 15 residues within 4Å: Chain A: D.177, S.178, L.179, I.182, R.207, A.212, I.213, K.214, T.220, K.221 Chain B: K.194, Y.236, A.237, D.238 Ligands: MG.4 16 PLIP interactions: 11 interactions with chain A, 5 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, B:D.238 Salt bridges: A:R.207, A:R.207, A:K.214, A:H.304, B:K.194, B:K.194 TTP.5: 16 residues within 4Å: Chain A: K.194, Y.236, A.237, D.238 Chain B: D.177, S.178, L.179, I.182, L.206, R.207, I.213, K.214, T.220, K.221, H.304 Ligands: MG.6 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.179, B:I.182, B:I.213, A:K.194 Hydrogen bonds: B:D.177, B:D.177, B:L.179, B:K.214, B:K.221, A:Y.236, A:D.238 Salt bridges: B:R.207, B:R.207, B:K.214, A:K.194, A:K.194

2 x MG: MAGNESIUM ION

MG.4: 3 residues within 4Å: Chain A: D.177, R.207 Ligands: TTP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: D.177 Ligands: TTP.5 No protein-ligand interaction detected (PLIP)

4 x MN: MANGANESE (II) ION

MN.9: 5 residues within 4Å: Chain C: E.118, E.185, E.219, H.222 Ligands: MN.10 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.10: 6 residues within 4Å: Chain C: D.87, E.118, H.122, F.189, E.219 Ligands: MN.9 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.11: 5 residues within 4Å: Chain D: E.118, E.185, E.219, H.222 Ligands: MN.12 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.12: 5 residues within 4Å: Chain D: D.87, E.118, H.122, E.219 Ligands: MN.11 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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