SMTL ID : 3s8b.1

Structure of Yeast Ribonucleotide Reductase 1 with AMPPNP and CDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 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, P.203, S.217, C.218, G.247, Q.288, N.426, C.428, E.430, L.445, M.606, P.607, T.608, A.609, S.610, T.611 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.202, A:S.202, A:S.202, A:S.202, A:G.247, A:Q.288, A:N.426, A:E.430, A:T.608, A:A.609, A:S.610, A:T.611 Water bridges: A:S.217, A:L.427, A:S.610 CDP.4: 17 residues within 4Å: Chain B: A.201, S.202, P.203, S.217, C.218, G.247, Q.288, N.426, C.428, E.430, L.445, M.606, P.607, T.608, A.609, S.610, T.611 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.202, B:S.202, B:S.202, B:S.202, B:G.247, B:Q.288, B:N.426, B:E.430, B:T.608, B:A.609, B:S.610, B:T.611 Water bridges: B:S.217, B:L.427, B:S.610

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

ANP.2: 13 residues within 4Å: Chain A: D.226, S.227, I.228, I.231, R.256, I.262, A.263, S.269 Chain B: K.243, Y.285, V.286, D.287 Ligands: MG.3 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.226, A:S.227, A:I.228, A:R.256, A:R.256, A:A.263, A:A.263, A:A.263, B:K.243, B:Y.285, B:Y.285, B:D.287, B:D.287 Water bridges: A:E.229, A:N.270, A:G.271 Salt bridges: B:K.243 ANP.5: 13 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, S.269 Ligands: MG.6 17 PLIP interactions: 6 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:K.243, A:Y.285, A:Y.285, A:D.287, A:D.287, B:D.226, B:S.227, B:I.228, B:R.256, B:R.256, B:A.263, B:A.263, B:A.263 Salt bridges: A:K.243 Water bridges: B:E.229, B:N.270, B:G.271

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., 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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