SMTL ID : 3hnd.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: TTP.2 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: TTP.8 No protein-ligand interaction detected (PLIP)

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

TTP.2: 20 residues within 4Å: Chain A: D.226, S.227, I.228, E.229, I.231, I.255, R.256, I.262, A.263, G.264, T.265, S.269, N.270 Chain B: K.243, Y.285, V.286, D.287, Q.288, G.289 Ligands: MG.1 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.228, A:I.231, A:I.262, A:T.265, B:K.243 Hydrogen bonds: A:D.226, A:I.228, A:R.256, A:A.263, A:G.264, A:T.265, A:S.269, A:N.270, B:Y.285, B:Q.288 Salt bridges: A:R.256, A:R.256, B:K.243, B:K.243 TTP.8: 19 residues within 4Å: Chain A: K.243, Y.285, V.286, D.287, Q.288, G.289 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 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.231, A:K.243 Hydrogen bonds: B:D.226, B:I.228, B:R.256, B:A.263, B:G.264, B:S.269, B:N.270, B:N.270, A:Y.285 Water bridges: B:E.229 Salt bridges: B:R.256, B:R.256, A:K.243, A:K.243

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 19 residues within 4Å: Chain A: S.202, S.217, C.218, A.245, G.246, G.247, G.295, A.296, N.427, L.428, C.429, E.431, L.446, M.602, P.603, T.604, A.605, S.606, T.607 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.202, A:S.202, A:G.246, A:N.427, A:E.431, A:A.605, A:S.606, A:T.607, A:T.607, A:T.607 GDP.9: 20 residues within 4Å: Chain B: A.201, S.202, S.217, C.218, A.245, G.246, G.247, R.293, A.296, N.427, L.428, C.429, E.431, L.446, M.602, P.603, T.604, A.605, S.606, T.607 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.202, B:S.202, B:S.202, B:S.217, B:A.245, B:R.293, B:N.427, B:E.431, B:A.605, B:S.606, B:T.607, B:T.607

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

SO4.4: 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:Y.137, A:D.138, A:D.138 SO4.5: 4 residues within 4Å: Chain A: N.614, E.615, T.621, Y.625 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.614, A:T.621, A:T.621 SO4.6: 3 residues within 4Å: Chain A: S.687, Q.688, K.689 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.689 SO4.10: 3 residues within 4Å: Chain B: S.687, Q.688, K.689 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.688, B:K.689

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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