SMTL ID : 6cgl.1

X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound as-isolated (pH 4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.1: 7 residues within 4Å: Chain A: V.33, H.34, F.37, N.42, R.90, F.91, R.117 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: 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 pi-Cation interactions: A:R.90 D5M.4: 8 residues within 4Å: Chain B: V.33, H.34, F.37, N.42, F.89, R.90, F.91, R.117 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.34, B:N.42, B:F.91, B:F.91 Salt bridges: B:R.90 pi-Stacking: B:F.37, B:F.37 pi-Cation interactions: B:R.90

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: T.153, T.581, G.582, S.583, I.584 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.153, A:T.153, A:G.582, A:S.583, A:I.584 SO4.3: 2 residues within 4Å: Chain A: V.367, K.530 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.530 SO4.5: 6 residues within 4Å: Chain B: T.153, P.580, T.581, G.582, S.583, I.584 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.153, B:T.153, B:T.153, B:G.582, B:S.583, B:I.584 SO4.6: 2 residues within 4Å: Chain B: V.367, K.530 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.530 SO4.7: 2 residues within 4Å: Chain B: Y.606, G.607 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parker, M.J. et al., An endogenous dAMP ligand inBacillus subtilisclass Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-05-09

Peptides

Ribonucleoside-diphosphate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase

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