SMTL ID : 7b9p.1

Structure of Ribonucleotide reductase from Rhodobacter sphaeroides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 15 residues within 4Å: Chain A: D.206, D.207, L.208, I.214, R.239, L.245, S.246, S.251, S.252, F.257 Chain B: K.226, A.267, I.268, K.269 Ligands: MG.2 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.214, A:F.257 Hydrogen bonds: A:D.206, A:D.207, A:L.208, A:R.239, A:S.246, A:S.246, A:S.251, A:S.252, B:K.226, B:K.269, B:K.269, B:G.272 Salt bridges: A:R.239, B:K.226, B:K.226 DTP.3: 15 residues within 4Å: Chain A: K.226, A.267, I.268, K.269 Chain B: D.206, D.207, L.208, I.214, R.239, L.245, S.246, S.251, S.252, F.257 Ligands: MG.4 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.214, B:F.257 Hydrogen bonds: B:D.206, B:L.208, B:R.239, B:S.246, B:S.246, B:S.251, B:S.252, A:K.226, A:K.269, A:K.269, A:G.272 Salt bridges: B:R.239, A:K.226, A:K.226

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: L.245, S.246 Chain B: K.226 Ligands: DTP.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: K.226 Chain B: L.245, S.246 Ligands: DTP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fietze, T. et al., HUG Domain Is Responsible for Active Dimer Stabilization in an NrdJd Ribonucleotide Reductase. Biochemistry (2022)

Release Date

2022-01-12

Peptides

Vitamin B12-dependent ribonucleotide reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Vitamin B12-dependent ribonucleotide reductase