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

Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae in Activated Form with Thiocyanate Bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: G.281, E.285 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.281, A:E.285, A:E.285, H2O.5 CA.6: 1 residues within 4Å: Chain B: S.146 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.146, H2O.9, H2O.10, H2O.10, H2O.13 CA.7: 2 residues within 4Å: Chain B: G.281, E.285 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.281, B:E.285, B:E.285, H2O.10, H2O.12

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain A: D.278 No protein-ligand interaction detected (PLIP) GOL.8: 2 residues within 4Å: Chain B: D.86, D.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.87 Water bridges: B:D.87

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 4 residues within 4Å: Chain B: F.259, L.262, D.263, P.306 No protein-ligand interaction detected (PLIP) SCN.4: 8 residues within 4Å: Chain B: L.102, D.103, Q.106, V.134, M.193, P.194, L.198, K.228 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.103 SCN.5: 5 residues within 4Å: Chain A: I.154, E.155 Chain B: Y.23, N.46, K.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.49 Water bridges: B:Y.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaesi, E.J. et al., Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-09-19

Peptides

Ribonucleoside-diphosphate reductase, beta subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase, beta subunit

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