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- PDB-8pwk: human HINT1 in complex with compound AT8003 -

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Basic information

Entry
Database: PDB / ID: 8pwk
Titlehuman HINT1 in complex with compound AT8003
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / complex intermediate compound inhibitor / Adenosine 5'-monophosphoramidase
Function / homology
Function and homology information


purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like superfamily
Similarity search - Domain/homology
: / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsZimberger, C. / Canard, B. / Ferron, F.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-0005 France
Citation
Journal: Plos Biol. / Year: 2024
Title: The activation chain of the broad-spectrum antiviral bemnifosbuvir at atomic resolution
Authors: Chazot, A. / Zimberger, C. / Feracci, M. / Moussa, A. / Good, S. / Sommadossi, J.P. / Alvarez, K. / Ferron, F. / Canard, B.
#1: Journal: Biorxiv / Year: 2024
Title: The activation chain of the broad-spectrum antiviral bemnifosbuvir at atomic resolution
Authors: Chazot, A. / Zimberger, C. / Feracci, M. / Moussa, A. / Good, S. / Sommadossi, J.P. / Alvarez, K. / Ferron, F. / Canard, B.
History
DepositionJul 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine triad nucleotide-binding protein 1
B: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0634
Polymers27,6482
Non-polymers4152
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-28 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.961, 46.45, 63.771
Angle α, β, γ (deg.)90, 94.98, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histidine triad nucleotide-binding protein 1 / Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting ...Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting protein 1 / PKCI-1


Mass: 13823.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-I0H / [(2~{R},3~{R},4~{R},5~{R})-5-[2-azanyl-6-(methylamino)purin-9-yl]-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate


Mass: 392.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18FN6O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 30-50% PEG 2K MME 0,1M Sodium cacodylate / PH range: 5.8-6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.095→39.864 Å / Num. obs: 12964 / % possible obs: 95.8 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.047 / Rrim(I) all: 0.125 / Net I/σ(I): 10.6
Reflection shellResolution: 2.095→2.132 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 657 / CC1/2: 0.904 / Rpim(I) all: 0.227 / Rrim(I) all: 0.592 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5 (20230222)data reduction
autoPROCdata scaling
MOLREP11.9.02; 28.02.2022phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.095→39.86 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.252 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.194
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 646 -RANDOM
Rwork0.19 ---
obs0.1926 12960 95.7 %-
Displacement parametersBiso mean: 25.67 Å2
Baniso -1Baniso -2Baniso -3
1--14.0107 Å20 Å27.6366 Å2
2--9.2193 Å20 Å2
3---4.7914 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.095→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 27 128 1911
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081845HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.952510HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d637SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes325HARMONIC5
X-RAY DIFFRACTIONt_it1827HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion232SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1626SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion15.61
LS refinement shellResolution: 2.1→2.12 Å
RfactorNum. reflection% reflection
Rfree0.3616 23 -
Rwork0.2181 --
obs0.2256 405 92.39 %

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