SMTL ID : 3hne.1

Crystal structure of human ribonucleotide reductase 1 bound to the effectors TTP and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

homo-dimer

Ligands

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

TTP.1: 18 residues within 4Å: Chain A: D.226, S.227, I.228, I.231, I.255, R.256, 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.2 15 PLIP interactions: 10 interactions with chain A, 5 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:D.287 Salt bridges: A:R.256, A:R.256, B:K.243, B:K.243 TTP.6: 18 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, T.265, S.269, N.270 Ligands: MG.7 18 PLIP interactions: 12 interactions with chain B, 6 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:N.270, B:N.270, A:Y.285, A:D.287, A:Q.288 Salt bridges: B:R.256, B:R.256, A:K.243, A:K.243

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

MG.2: 2 residues within 4Å: Chain A: S.227 Ligands: TTP.1 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: TTP.6 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: R.6 Ligands: ATP.8 No protein-ligand interaction detected (PLIP)

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

SO4.3: 4 residues within 4Å: Chain A: I.135, I.136, Y.137, D.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.137, A:D.138 SO4.4: 3 residues within 4Å: Chain A: S.687, Q.688, K.689 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.687, A:Q.688, A:K.689 Salt bridges: A:K.689 SO4.5: 6 residues within 4Å: Chain A: A.201, S.202, T.604, A.605, S.606, T.607 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.202, A:S.202, A:A.605, A:S.606, A:T.607 SO4.11: 3 residues within 4Å: Chain B: S.687, Q.688, K.689 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.687, B:Q.688, B:K.689 Salt bridges: B:K.689 SO4.12: 3 residues within 4Å: Chain B: H.87, K.92, R.166 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.87, B:K.92, B:R.166 SO4.13: 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.202, B:A.605, B:S.606, B:T.607

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.8: 15 residues within 4Å: Chain B: V.3, K.5, R.6, E.11, R.12, M.14, K.17, I.18, R.21, T.53, L.56, D.57, K.88 Ligands: MG.9, MG.10 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:K.5, B:R.6, B:E.11, B:E.11, B:M.14, B:K.17, B:R.21, B:T.53, B:D.57 Salt bridges: B:K.5, B:K.5, B:K.5, B:R.6, B:K.17, B:K.88

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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