SMTL ID : 6cgn.1 (1 other biounit)

X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound (pH 7)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

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

DA.1: 8 residues within 4Å: Chain A: V.33, H.34, F.37, N.42, R.90, F.91, R.117 Ligands: PO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.42, A:F.91, A:F.91, A:R.117 Salt bridges: A:R.90 pi-Stacking: A:F.37

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: K.88, R.90 Ligands: DA.1 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.88, A:R.90

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: G.476, I.477, A.478, S.481, E.483, K.542 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.478, A:S.481 EDO.4: 7 residues within 4Å: Chain A: A.347, R.350, L.656, L.658, L.667, D.671, I.682 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.350 EDO.5: 4 residues within 4Å: Chain A: E.65, E.66, E.67, K.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.66, A:E.67

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonucleoside-diphosphate reductase

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