SMTL ID : 2cvy.1

Structures of Yeast Ribonucleotide Reductase I

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x PHE- THR- PHE- ASN- GLU- ASP- PHE: 9-per peptide from Ribonucleoside-diphosphate reductase small chain 1(Non-covalent)

PHE-THR-PHE-ASN-GLU-ASP-PHE.1: 15 residues within 4Å: Chain A: V.342, E.343, Q.386, Y.390, S.691, Q.692, K.693, M.721, G.722, K.723, T.725, S.726, M.727, F.729, Y.730 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.390, A:Y.390, A:Q.692, A:M.721, A:T.725, A:M.727, A:Y.730 Hydrogen bonds: A:Q.386, A:Q.692, A:S.726, A:S.726 pi-Stacking: A:W.389, A:F.729 PHE-THR-PHE-ASN-GLU-ASP-PHE.4: 15 residues within 4Å: Chain B: V.342, E.343, Q.386, Y.390, S.691, Q.692, K.693, M.721, G.722, K.723, T.725, S.726, M.727, F.729, Y.730 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.390, B:Y.390, B:Q.692, B:M.721, B:T.725, B:M.727, B:Y.730 Hydrogen bonds: B:Q.386, B:Q.692, B:S.726, B:S.726 pi-Stacking: B:W.389, B:F.729

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

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

2 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.3: 16 residues within 4Å: Chain A: D.226, S.227, I.228, E.229, I.231, I.255, R.256, Y.261, I.262, A.263, S.269, N.270 Chain B: K.243, Y.285, V.286 Ligands: MG.2 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.228, A:I.228, A:I.231, B:K.243 Hydrogen bonds: A:D.226, A:I.228, A:A.263, A:N.270, B:Y.285 Water bridges: A:S.269, A:S.269, B:Y.285 Salt bridges: A:R.256, A:R.256, B:K.243, B:K.243 TTP.6: 16 residues within 4Å: Chain A: K.243, Y.285, V.286 Chain B: D.226, S.227, I.228, E.229, I.231, I.255, R.256, Y.261, I.262, A.263, S.269, N.270 Ligands: MG.5 16 PLIP interactions: 5 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:K.243, B:I.228, B:I.228, B:I.231 Hydrogen bonds: A:Y.285, B:D.226, B:I.228, B:A.263, B:N.270 Water bridges: A:Y.285, B:S.269, B:S.269 Salt bridges: A:K.243, A:K.243, B:R.256, B:R.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, H. et al., Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-03-07

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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