SMTL ID : 3k8t.1

Structure of eukaryotic rnr large subunit R1 complexed with designed adp analog compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

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

2 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.2: 17 residues within 4Å: Chain A: D.226, S.227, I.228, I.231, R.256, I.262, A.263, G.264, N.270 Chain B: K.243, Y.285, V.286, D.287, Q.288, G.289, G.290 Ligands: MG.1 23 PLIP interactions: 11 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:I.228, A:I.231 Hydrogen bonds: A:D.226, A:I.228, A:A.263, A:G.264, B:Y.285, B:Y.285, B:D.287, B:D.287, B:G.289, B:G.290 Water bridges: A:E.229, A:R.256, A:R.256, B:Y.285 Salt bridges: A:R.256, A:R.256, B:K.111, B:K.243, B:K.243, B:D.287 pi-Cation interactions: B:Y.285 DGT.6: 17 residues within 4Å: Chain A: K.243, Y.285, V.286, D.287, Q.288, G.289, G.290 Chain B: D.226, S.227, I.228, I.231, R.256, I.262, A.263, G.264, N.270 Ligands: MG.5 23 PLIP interactions: 11 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:I.228, B:I.231 Hydrogen bonds: B:D.226, B:I.228, B:A.263, B:G.264, A:Y.285, A:Y.285, A:D.287, A:D.287, A:G.289, A:G.290 Water bridges: B:E.229, B:R.256, B:R.256, A:Y.285 Salt bridges: B:R.256, B:R.256, A:K.111, A:K.243, A:K.243, A:D.287 pi-Cation interactions: A:Y.285

2 x 2A5: 2'-deoxy-2'-(2-hydroxyethyl)adenosine 5'-(trihydrogen diphosphate)(Non-covalent)

2A5.3: 20 residues within 4Å: Chain A: A.201, S.202, S.217, C.218, F.219, G.246, G.247, I.248, A.296, N.426, L.427, C.428, E.430, L.445, M.606, P.607, T.608, A.609, S.610, T.611 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.427 Hydrogen bonds: A:S.202, A:S.202, A:F.219, A:F.219, A:G.246, A:N.426, A:L.427, A:E.430, A:T.608, A:A.609, A:S.610, A:T.611 2A5.7: 20 residues within 4Å: Chain B: A.201, S.202, S.217, C.218, F.219, G.246, G.247, I.248, A.296, N.426, L.427, C.428, E.430, L.445, M.606, P.607, T.608, A.609, S.610, T.611 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.427 Hydrogen bonds: B:S.202, B:S.202, B:F.219, B:F.219, B:G.246, B:N.426, B:L.427, B:E.430, B:T.608, B:A.609, B:S.610, B:T.611

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: D.336, R.412, W.732, K.733 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.732 GOL.8: 4 residues within 4Å: Chain B: D.336, R.412, W.732, K.733 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.732

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, D. et al., Structure-Based Design, Synthesis, and Evaluation of 2'-(2-Hydroxyethyl)-2'-deoxyadenosine and the 5'-Diphosphate Derivative as Ribonucleotide Reductase Inhibitors. Chemmedchem (2009)

Release Date

2010-03-02

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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