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RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH SUBSTRATE, GDP AND EFFECTOR DTTP FROM ESCHERICHIA COLI

X-ray diffraction
3.2Å resolution
PDB entry 4r1r coloured by chain, front view.
PDB entry 4r1r coloured by chain, side view.
PDB entry 4r1r coloured by chain, top view.
Source organism: Escherichia coli
Assemblies composition:
hetero trimer
hetero dimer (preferred)
hetero pentadecamer
hetero dodecamer
hetero pentamer
hetero tetramer
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1
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Assembly Name: Ribonucleoside-diphosphate reductase 1
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Multimeric state: hetero trimer
Accessible surface area: 29084.44 Å2
Buried surface area: 3528.44 Å2
Dissociation area: 249.75 Å2
Dissociation energy (ΔGdiss): 0.08 kcal/mol
Dissociation entropy (TΔSdiss): 4.65 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-132527
Assembly 10
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Assembly Name: Ribonucleoside-diphosphate reductase 1
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Multimeric state: hetero dimer
Accessible surface area: 28957.56 Å2
Buried surface area: 3028.93 Å2
Dissociation area: 880.46 Å2
Dissociation energy (ΔGdiss): 8.95 kcal/mol
Dissociation entropy (TΔSdiss): 8.85 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-132526
Assembly 2 (preferred)
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Assembly Name: Ribonucleoside-diphosphate reductase 1
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Multimeric state: hetero dimer
Accessible surface area: 28956.64 Å2
Buried surface area: 3027.24 Å2
Dissociation area: 877.01 Å2
Dissociation energy (ΔGdiss): 8.9 kcal/mol
Dissociation entropy (TΔSdiss): 8.85 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-132526
Assembly 3
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Assembly Name: Ribonucleoside-diphosphate reductase 1
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Multimeric state: hetero dimer
Accessible surface area: 28973.17 Å2
Buried surface area: 3026.94 Å2
Dissociation area: 878.76 Å2
Dissociation energy (ΔGdiss): 8.97 kcal/mol
Dissociation entropy (TΔSdiss): 8.85 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-132526
Assembly 4
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Assembly Name: Ribonucleoside-diphosphate reductase 1
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Multimeric state: hetero pentadecamer
Accessible surface area: 155485.83 Å2
Buried surface area: 38304.41 Å2
Dissociation area: 249.75 Å2
Dissociation energy (ΔGdiss): 0.08 kcal/mol
Dissociation entropy (TΔSdiss): 4.65 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-132535
Assembly 5
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Assembly Name: Ribonucleoside-diphosphate reductase 1
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Multimeric state: hetero dodecamer
Accessible surface area: 155631.39 Å2
Buried surface area: 36374.88 Å2
Dissociation area: 4,543.5 Å2
Dissociation energy (ΔGdiss): 9.5 kcal/mol
Dissociation entropy (TΔSdiss): 18.58 kcal/mol
Symmetry number: 6
PDBe Complex ID: PDB-CPX-132534
Assembly 6
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Assembly Name: Ribonucleoside-diphosphate reductase 1
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Multimeric state: hetero pentamer
Accessible surface area: 54978.11 Å2
Buried surface area: 9618.64 Å2
Dissociation area: 249.75 Å2
Dissociation energy (ΔGdiss): 0.46 kcal/mol
Dissociation entropy (TΔSdiss): 4.28 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-132529
Assembly 7
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Assembly Name: Ribonucleoside-diphosphate reductase 1 complex
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Multimeric state: hetero tetramer
Accessible surface area: 54929.36 Å2
Buried surface area: 9074.99 Å2
Dissociation area: 3,272.41 Å2
Dissociation energy (ΔGdiss): 11.64 kcal/mol
Dissociation entropy (TΔSdiss): 33.37 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-132528
Complex Portal ID: CPX-1075
Assembly 8
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Assembly Name: Ribonucleoside-diphosphate reductase 1
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Multimeric state: hetero dodecamer
Accessible surface area: 155105.28 Å2
Buried surface area: 36806.82 Å2
Dissociation area: 4,611 Å2
Dissociation energy (ΔGdiss): 8.89 kcal/mol
Dissociation entropy (TΔSdiss): 18.59 kcal/mol
Symmetry number: 6
PDBe Complex ID: PDB-CPX-132534
Assembly 9
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Assembly Name: Ribonucleoside-diphosphate reductase 1 complex
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Multimeric state: hetero tetramer
Accessible surface area: 54851.23 Å2
Buried surface area: 9119.14 Å2
Dissociation area: 3,295.13 Å2
Dissociation energy (ΔGdiss): 11.36 kcal/mol
Dissociation entropy (TΔSdiss): 33.37 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-132528
Complex Portal ID: CPX-1075

Macromolecules

Ribonucleoside-diphosphate reductase 1 subunit alpha
Chains: A, B, C
Length: 761 amino acids
Theoretical weight: 85.85 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P00452 (Residues: 1-761; Coverage: 100%)
Gene names: JW2228, b2234, dnaF, nrdA
Pfam:
InterPro:
CATH: Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
SCOP:
Ribonucleoside-diphosphate reductase 1 subunit alpha in PDB entry 4r1r, assembly 2, front view.
Ribonucleoside-diphosphate reductase 1 subunit alpha in PDB entry 4r1r, assembly 2, side view.
Ribonucleoside-diphosphate reductase 1 subunit alpha in PDB entry 4r1r, assembly 2, top view.
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Ribonucleoside-diphosphate reductase 1 subunit beta
Chains: D, E, F, P
Length: 20 amino acids
Theoretical weight: 2.27 KDa
Source organism: Escherichia coli
Expression system: Not provided
UniProt:
  • Canonical: P69924 (Residues: 357-376; Coverage: 5%)
Gene names: JW2229, b2235, ftsB, nrdB
Ribonucleoside-diphosphate reductase 1 subunit beta in PDB entry 4r1r, assembly 2, front view.
Ribonucleoside-diphosphate reductase 1 subunit beta in PDB entry 4r1r, assembly 2, side view.
Ribonucleoside-diphosphate reductase 1 subunit beta in PDB entry 4r1r, assembly 2, top view.
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