SMTL ID : 3hnc.1

Crystal structure of human ribonucleotide reductase 1 bound to the effector TTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: D.226, S.227 Ligands: TTP.2 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: TTP.7 No protein-ligand interaction detected (PLIP)

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

TTP.2: 19 residues within 4Å: Chain A: D.226, S.227, I.228, I.231, I.255, R.256, Y.261, I.262, A.263, G.264, S.269, N.270 Chain B: K.243, Y.285, V.286, D.287, Q.288, G.289 Ligands: MG.1 22 PLIP interactions: 14 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:I.228, A:I.231, B:K.243 Hydrogen bonds: A:D.226, A:I.228, A:A.263, A:G.264, A:N.270, A:N.270, B:Y.285, B:Y.285, B:D.287, B:Q.288, B:G.289 Water bridges: A:E.229, A:R.256, A:R.256, A:G.271 Salt bridges: A:R.256, A:R.256, B:K.243, B:K.243 TTP.7: 17 residues within 4Å: Chain A: K.243, Y.285, V.286, D.287, Q.288 Chain B: D.226, S.227, I.228, I.231, I.255, R.256, I.262, A.263, G.264, S.269, N.270 Ligands: MG.6 22 PLIP interactions: 17 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.228, B:I.231, B:I.262, A:K.243 Hydrogen bonds: B:D.226, B:I.228, B:R.256, B:A.263, B:G.264, B:T.265, B:N.270, B:N.270, A:Y.285, A:D.287 Water bridges: B:E.229, B:R.256, B:R.256, B:G.271 Salt bridges: B:R.256, B:R.256, A:K.243, A:K.243

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: I.135, I.136, Y.137, D.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.135, A:Y.137, A:D.138 SO4.4: 3 residues within 4Å: Chain A: S.687, Q.688, K.689 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.688, A:K.689 SO4.5: 5 residues within 4Å: Chain A: A.201, S.202, T.604, S.606, T.607 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.202, A:S.606, A:T.607 Water bridges: A:T.604, A:A.605 SO4.8: 3 residues within 4Å: Chain B: S.687, Q.688, K.689 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.687, B:Q.688, B:K.689 Water bridges: B:S.687, B:K.689, B:K.689 Salt bridges: B:K.689 SO4.9: 3 residues within 4Å: Chain B: K.5, R.6, T.53 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.6, B:T.53 Water bridges: B:D.7 Salt bridges: B:R.6 SO4.10: 7 residues within 4Å: Chain B: A.201, S.202, P.603, T.604, A.605, S.606, T.607 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.202, B:S.202, B:S.606, B:T.607 Water bridges: B:A.605, B:A.605

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fairman, J.W. et al., Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization. Nat.Struct.Mol.Biol. (2011)

Release Date

2011-02-23

Peptides

Ribonucleoside-diphosphate reductase large subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase large subunit

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