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- PDB-9qtc: HINT1 complexed with GS-441524 -

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Basic information

Entry
Database: PDB / ID: 9qtc
TitleHINT1 complexed with GS-441524
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsTRANSFERASE / complex
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 / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity ...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 / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling / protein kinase C binding / cytoskeleton / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / nucleotide binding / hydrolase activity / 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
Chem-U08 / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZimberger, C. / Ferron, F.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)IA-10-INBS-0005 France
Other privateXPLORE France
CitationJournal: Structure / Year: 2026
Title: Impact of remdesivir modifications on human HINT1 binding - A structural and functional study in the remdesivir activation pathway.
Authors: Chazot, A. / Zimberger, C. / Fotopoulos, I. / Canard, B. / Alvarez, K. / Ferron, F.
History
DepositionApr 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: 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)28,1344
Polymers27,6482
Non-polymers4872
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-16 kcal/mol
Surface area9760 Å2
Unit cell
Length a, b, c (Å)78.286, 46.326, 64.066
Angle α, β, γ (deg.)90, 94.66, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-202-

MES

21A-202-

MES

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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-U08 / (2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolane-2-carbonitrile / Remdesivir, reacted form


Mass: 291.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13N5O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: antivirus*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES , 27% to 30% PEG 8000 / PH range: 6.1-6.5

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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 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.3→39.013 Å / Num. obs: 56318 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.047 / Rrim(I) all: 0.121 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.527-39.0136.40.08316.129180.9930.0350.09100
1.3-1.32250.5262.527420.8530.2510.58698

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→39.01 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.05 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.053 / SU Rfree Blow DPI: 0.053 / SU Rfree Cruickshank DPI: 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 2767 -RANDOM
Rwork0.1704 53551 --
obs0.1713 56318 99.9 %-
Displacement parametersBiso mean: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1--5.3697 Å20 Å20.3659 Å2
2--2.8041 Å20 Å2
3---2.5656 Å2
Refine analyzeLuzzati coordinate error obs: 0.148 Å
Refinement stepCycle: LAST / Resolution: 1.3→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 33 318 2107
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112110HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.172891HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d772SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes377HARMONIC5
X-RAY DIFFRACTIONt_it2110HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion270SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2383SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.48
X-RAY DIFFRACTIONt_other_torsion16.54
LS refinement shellResolution: 1.3→1.31 Å
RfactorNum. reflection% reflection
Rfree0.2682 49 -
Rwork0.268 1078 -
obs0.268 1127 95.87 %

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