SMTL ID : 3s8c.1

Structure of Yeast Ribonucleotide Reductase 1 R293A with AMPPNP and CDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 15 residues within 4Å: Chain A: D.226, S.227, I.228, I.231, R.256, I.262, A.263, N.270 Chain B: K.243, Y.285, V.286, D.287, Q.288, G.289 Ligands: MG.2 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:D.287, A:D.226, A:I.228, A:R.256, A:R.256, A:A.263, A:A.263 Salt bridges: B:K.243 Water bridges: A:S.227, A:E.229 ANP.4: 15 residues within 4Å: Chain A: K.243, Y.285, V.286, D.287, Q.288, G.289 Chain B: D.226, S.227, I.228, I.231, R.256, I.262, A.263, N.270 Ligands: MG.5 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.226, B:I.228, B:R.256, B:R.256, B:A.263, B:A.263, A:D.287 Water bridges: B:E.229, A:K.243 Salt bridges: A:K.243

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.227 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: S.227 Ligands: ANP.4 No protein-ligand interaction detected (PLIP)

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

CDP.3: 17 residues within 4Å: Chain A: A.201, S.202, P.203, F.206, S.217, A.245, G.246, G.247, K.292, L.427, C.428, M.606, P.607, T.608, A.609, S.610, T.611 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.202, A:S.202, A:S.202, A:G.246, A:G.247, A:N.291, A:T.608, A:A.609, A:S.610, A:T.611 CDP.6: 17 residues within 4Å: Chain B: A.201, S.202, P.203, F.206, S.217, A.245, G.246, G.247, K.292, L.427, C.428, M.606, P.607, T.608, A.609, S.610, T.611 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.202, B:S.202, B:S.202, B:G.246, B:G.247, B:N.291, B:T.608, B:A.609, B:S.610, B:T.611

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, M.F. et al., Structural and biochemical basis of lethal mutant R293A of yeast ribonucleotide reductase. To be Published

Release Date

2012-04-11

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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