SMTL ID : 3hnf.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.16 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: R.256 Ligands: TTP.2 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: D.226 Ligands: TTP.6 No protein-ligand interaction detected (PLIP)

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

TTP.2: 13 residues within 4Å: Chain A: D.226, S.227, I.228, R.256, I.262, A.263, G.264, T.265, S.269 Chain B: K.243, V.286, D.287 Ligands: MG.1 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.228, A:I.262, A:T.265, B:K.243 Hydrogen bonds: A:D.226, A:I.228, A:A.263, A:G.264, B:D.287 Salt bridges: A:R.256, A:R.256, B:K.243, B:K.243 TTP.6: 15 residues within 4Å: Chain A: K.243, V.286, D.287, Q.288 Chain B: D.226, S.227, I.228, I.231, R.256, I.262, A.263, G.264, T.265, S.269 Ligands: MG.5 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.228, B:I.228, B:I.231, B:T.265, A:K.243 Hydrogen bonds: B:D.226, B:I.228, B:A.263, B:G.264, A:D.287, A:Q.288 Salt bridges: B:R.256, B:R.256, A:K.243, A:K.243

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

SO4.3: 6 residues within 4Å: Chain A: A.201, S.202, T.604, A.605, S.606, T.607 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.202, A:S.202, A:S.606, A:T.607 SO4.4: 3 residues within 4Å: Chain A: I.136, Y.137, D.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.137, A:D.138 SO4.8: 6 residues within 4Å: Chain B: S.202, P.603, T.604, A.605, S.606, T.607 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.202, B:S.202, B:S.202, B:A.605, B:S.606, B:T.607 Water bridges: B:T.607 SO4.9: 4 residues within 4Å: Chain B: I.686, 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

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.7: 13 residues within 4Å: Chain B: V.3, K.5, R.6, E.11, R.12, V.13, M.14, K.17, I.18, R.21, T.53, L.56, K.88 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.6, B:E.11, B:M.14, B:T.53 Salt bridges: B:K.5, B:K.5, B:R.6, B:R.21, B:K.88, B:K.88, 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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