SMTL ID : 3tb9.1

Structure of Yeast Ribonucleotide Reductase 1 Q288A with AMPPNP and CDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-dimer

Ligands

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.1: 17 residues within 4Å: Chain A: A.201, S.202, S.217, C.218, G.246, G.247, N.426, L.427, C.428, E.430, L.445, M.606, P.607, T.608, A.609, S.610, T.611 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.202, A:S.202, A:S.202, A:G.247, A:N.426, A:E.430, A:T.608, A:A.609, A:S.610, A:T.611 Water bridges: A:F.219 CDP.4: 17 residues within 4Å: Chain B: A.201, S.202, S.217, C.218, G.246, G.247, N.426, L.427, C.428, E.430, L.445, M.606, P.607, T.608, A.609, S.610, T.611 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.202, B:S.202, B:S.202, B:G.247, B:N.426, B:E.430, B:T.608, B:A.609, B:S.610, B:T.611 Water bridges: B:F.219

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 12 residues within 4Å: Chain A: D.226, S.227, I.228, I.231, R.256, I.262, A.263 Chain B: K.243, Y.285, V.286, D.287 Ligands: MG.3 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:K.243, B:D.287, B:D.287, A:D.226, A:I.228, A:R.256, A:R.256, A:A.263, A:A.263, A:A.263 Water bridges: B:Y.285, B:Y.285, B:Y.285, A:T.265 Salt bridges: B:K.243 ANP.5: 12 residues within 4Å: Chain A: K.243, Y.285, V.286, D.287 Chain B: D.226, S.227, I.228, I.231, R.256, I.262, A.263 Ligands: MG.6 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:K.243, A:D.287, A:D.287, B:D.226, B:I.228, B:R.256, B:R.256, B:A.263, B:A.263, B:A.263 Water bridges: A:Y.285, A:Y.285, A:Y.285, B:T.265 Salt bridges: A:K.243

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 1 residues within 4Å: Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: ANP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, M.F. et al., Role of Arginine 293 and Glutamine 288 in Communication between Catalytic and Allosteric Sites in Yeast Ribonucleotide Reductase. J.Mol.Biol. (2012)

Release Date

2012-04-04

Peptides

Ribonucleoside-diphosphate reductase large chain 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribonucleoside-diphosphate reductase large chain 1

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