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- PDB-4x3v: Crystal structure of human ribonucleotide reductase 1 bound to in... -

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Basic information

Entry
Database: PDB / ID: 4x3v
TitleCrystal structure of human ribonucleotide reductase 1 bound to inhibitor
ComponentsRibonucleoside-diphosphate reductase large subunit
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Complex / reducatse / inhibitor / enzyme / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / positive regulation of G0 to G1 transition / mitochondrial DNA replication / Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase ...ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / positive regulation of G0 to G1 transition / mitochondrial DNA replication / Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein heterotetramerization / response to ionizing radiation / DNA synthesis involved in DNA repair / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / centriolar satellite / male gonad development / disordered domain specific binding / nuclear envelope / retina development in camera-type eye / ciliary basal body / DNA repair / neuronal cell body / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal ...ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-3X4 / THYMIDINE-5'-TRIPHOSPHATE / Ribonucleoside-diphosphate reductase large subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsDealwis, C.G. / Ahmad, M.F. / Alam, I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100887-01 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA100827-04A1 United States
CitationJournal: J.Med.Chem. / Year: 2015
Title: Identification of Non-nucleoside Human Ribonucleotide Reductase Modulators.
Authors: Ahmad, M.F. / Huff, S.E. / Pink, J. / Alam, I. / Zhang, A. / Perry, K. / Harris, M.E. / Misko, T. / Porwal, S.K. / Oleinick, N.L. / Miyagi, M. / Viswanathan, R. / Dealwis, C.G.
History
DepositionDec 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase large subunit
B: Ribonucleoside-diphosphate reductase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,7415
Polymers180,3582
Non-polymers1,3833
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-16 kcal/mol
Surface area49870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.880, 110.498, 216.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonucleoside-diphosphate reductase large subunit / Ribonucleoside-diphosphate reductase subunit M1 / Ribonucleotide reductase large subunit


Mass: 90179.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRM1, RR1 / Production host: Escherichia coli (E. coli)
References: UniProt: P23921, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Chemical ChemComp-3X4 / N~6~-{N-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)acetyl]-2-methyl-D-alanyl}-D-lysine


Mass: 418.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N4O6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.9
Details: 0.1 M Tris-HCl pH 7.9, 0.2 M LiSO4, 19% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.7→200 Å / Num. obs: 19866 / % possible obs: 95.6 % / Redundancy: 3.2 % / Net I/σ(I): 32.6
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HNC

3hnc


Resolution: 3.7→108.361 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2892 1834 10.01 %
Rwork0.2323 --
obs0.2381 18327 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→108.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11296 0 88 0 11384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911634
X-RAY DIFFRACTIONf_angle_d1.78815836
X-RAY DIFFRACTIONf_dihedral_angle_d19.0294184
X-RAY DIFFRACTIONf_chiral_restr0.0741785
X-RAY DIFFRACTIONf_plane_restr0.0082027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7003-3.80040.40721440.33651289X-RAY DIFFRACTION98
3.8004-3.91220.39261400.29531262X-RAY DIFFRACTION98
3.9122-4.03850.32511400.28791261X-RAY DIFFRACTION97
4.0385-4.18290.30811390.27381258X-RAY DIFFRACTION97
4.1829-4.35030.33631410.25151254X-RAY DIFFRACTION97
4.3503-4.54830.2911400.2491261X-RAY DIFFRACTION95
4.5483-4.78810.33021400.25641259X-RAY DIFFRACTION96
4.7881-5.08810.3381400.25371262X-RAY DIFFRACTION96
5.0881-5.4810.28571400.23971267X-RAY DIFFRACTION96
5.481-6.03250.31221410.24281264X-RAY DIFFRACTION95
6.0325-6.90530.30231400.23291261X-RAY DIFFRACTION95
6.9053-8.69930.25581420.19151277X-RAY DIFFRACTION95
8.6993-108.40690.20961470.17351318X-RAY DIFFRACTION91

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